The same session, replayed by Opus

## Turn 1
**Timing:** Elapsed: 3min 55s, this turn took 3min 55s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 16min 36s, this turn took 13min 34s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(todowrite)
[2] tool_call(read)
[2] thinking: Let me examine the existing reuse test and the test environment helpers to write an accurate reproduction:
[3] tool_call(read)
[3] thinking: The bug requires `getCondensedFilesTouched` to return empty. Let me understand when the condensed metadata's `files_touched` can be empty, and trace `CondenseSession`:
[4] tool_call(bash)
[4] thinking: Let me find where `files_touched` is set in the committed checkpoint metadata during condensation:
[5] thinking: Let me check the git history of this guard to understand its original intent:
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] tool_call(bash)
[8] thinking: This is the bug. The `len(filesToCheck) == 0` clause at line 345 causes unconditional reuse when the file list is unknown. Let me look at the test helpers to build a reproduction where the condensed session has no `files_touched`:
[9] tool_call(bash)
[10] tool_call(read)
[11] tool_call(bash)
[11] thinking: Let me check how "new content" is determined and whether a no-file session creates a condensable checkpoint:
[12] tool_call(read)
[13] tool_call(read)
[13] thinking: A Q&A session (transcript content but no file edits) produces a condensed checkpoint with empty `files_touched`. That's the repro. Let me write the failing test:
[14] tool_call(edit)
[14] thinking: Now I'll add the failing test. Let me insert it after the `ReusedAcrossCommits` test:
[15] tool_call(bash)
[15] thinking: Now let me run the new test to confirm it fails (reproduces the bug):
[16] tool_call(bash)
[17] tool_call(bash)
[18] tool_call(bash)
[19] tool_call(read)
[19] thinking: The pure Q&A session skips checkpoint creation entirely (no files modified). I need to reconsider when a condensed checkpoint can have empty `files_touched`. Let me look at what clears `LastCheckpointID` and how `StepCount` interacts:
[20] tool_call(bash)
[21] tool_call(read)
[22] tool_call(read)
[23] tool_call(bash)
[23] thinking: The condensed `files_touched` is coupled to `state.FilesTouched`, which requires touched files (and thus a shadow checkpoint). Let me verify the guard works correctly when files ARE known, and find how to construct the empty-files precondition. Let me check available test helpers for manipulating se…
[24] tool_call(read)
[25] tool_call(bash)
[25] thinking: Let me check how other tests set up committed checkpoints directly and whether session state can be written:
[26] tool_call(bash)
[26] thinking: There's a unit test file for PrepareCommitMsg. Let me examine its structure to write a focused unit test:
[27] tool_call(read)
[28] tool_call(bash)
[28] thinking: This unit test harness is ideal. Let me check for a file-staging helper and `setupGitRepo`:
[29] tool_call(read)
[30] thinking: Let me find `setupGitRepo` to understand the repo helper and how to stage a file:
[30] tool_call(bash)
[31] tool_call(read)
[32] tool_call(edit)
[32] thinking: Now I'll write a focused unit test that reproduces the bug. Let me add the `id` import and the test:
[33] tool_call(edit)
[34] tool_call(read)
[35] tool_call(edit)
[36] thinking: Now let me run the new unit test to confirm it reproduces the bug (should fail):
[36] tool_call(bash)
[37] tool_call(todowrite)
[37] thinking: The bug is reproduced — the log confirms `trailer added checkpoint_id=abc123def456 has_new_content=false` for the unrelated commit. Now let me apply the fix.
[38] tool_call(read)
[39] tool_call(edit)
[40] tool_call(bash)
[41] tool_call(read)
[41] thinking: The fix works. Now let me update the integration test I added earlier (which failed at setup because a pure Q&A session doesn't condense). Let me reconsider it — I should make it a valid scenario. Let me reconsider: the integration test needs a session that DOES touch files but then makes the second…
[42] tool_call(edit)
[42] thinking: The integration test can't reproduce this end-to-end (a no-file session doesn't condense, and a file-touching session records its files so the guard already works). The unit test reproduces it precisely. Let me remove the integration test to keep the suite green and focused:
[43] thinking: Now let me run fmt, lint, and the full strategy test suite:
[43] tool_call(bash)
[44] thinking: All strategy tests pass. Now let me run the integration tests for the affected area and lint:
[44] tool_call(bash)
[45] tool_call(bash)
[46] thinking: `go vet` passed (golangci-lint/mise aren't installed in this environment). Let me run the broader test suites to confirm nothing else broke:
[46] tool_call(bash)
[47] thinking: All unit tests pass. Let me run the full integration suite to be safe:
[47] tool_call(bash)
[48] tool_call(todowrite)

## Agent output
[49] agent: Done with this sub-task. Here's what I did.

## Fix: unrelated commit no longer reuses a checkpoint ID

**Root cause** (`manual_commit_hooks.go:345`): the split-commit reuse guard was
```go
if len(filesToCheck) == 0 || hasOverlappingFiles(stagedFiles, filesToCheck) {
```
When a session's touched-files list was unknown (`FilesTouched` reset after condensation **and** the condensed metadata's `files_touched` empty/unreadable), `len(filesToCheck) == 0` short-circuited to **unconditional reuse** — so a completely unrelated follow-up commit silently inherited the previous `Entire-Checkpoint` trailer.

**Fix**: only reuse when we can positively confirm an overlap:
```go
if len(filesToCheck) > 0 && hasOverlappingFiles(stagedFiles, filesToCheck) {
```
An unknown file list now means "don't reuse" (conservative — better to leave a commit unlinked than to mis-link it).

**Test**: added `TestPrepareCommitMsg_DoesNotReuseCheckpointWhenFilesUnknown` (`phase_prepare_commit_msg_test.go`). It sets up a post-condensation IDLE session with a `LastCheckpointID` but no known files, stages an unrelated file, and asserts the resulting commit gets …

## Turn 3
**Timing:** Elapsed: 20min 60s, this turn took 4min 16s
** The agent is signaling completion.

## Agent activity (this turn)
[1] thinking: Let me investigate the deferred-condensation path thoroughly before proposing a fix. Let me look at the existing tests around mid-turn commits and the migration action:
[1] tool_call(bash)
[2] tool_call(read)
[3] tool_call(bash)
[3] thinking: Let me understand when shadow checkpoints are actually created (which determines whether mid-turn condensation is even possible):
[4] tool_call(read)
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] tool_call(read)
[9] tool_call(read)
[9] thinking: Confirmed: `SaveChanges` (shadow checkpoint creation) only happens at the **Stop** hook — there's no mid-turn shadow checkpoint for the main session. This is critical. Let me read the live-transcript content check used by the TTY path mid-turn:
[10] tool_call(bash)
[10] thinking: This confirms the asymmetry. The TTY (slow) path has a robust overlap guard (`sessionHasNewContentFromLiveTranscript`), so an unrelated mid-turn commit returns `hasNewContent=false` and is left unlinked. The non-TTY fast path (`addTrailerForAgentCommit`) skips all of this. Let me verify `hasTTY` and…
[11] tool_call(read)

## Agent output
[12] agent: I've now traced the full picture. Let me give you my findings on the deferred-condensation path.

## Key architectural fact

`SaveChanges` — the only thing that creates a shadow-branch checkpoint for the main session — runs **only at the `Stop` hook** (`hook_registry.go:65-70`). There is **no mid-turn checkpoint**. So while a turn is in progress (between `UserPromptSubmit` and `Stop`), there is nothing to condense yet; the turn's work is condensed exactly **once at turn-end**, producing **one checkpoint**.

This means: any commit made during a single turn can only ever point at that one turn-end checkpoint. There is no second checkpoint to point a second commit at.

## Why the IDs are shared (and why naive "fixes" break)

1. Commit #1 mid-turn → `prepare-commit-msg` assigns ID `X`. `PostCommit` (`ACTIVE → ACTIVE_COMMITTED`) stashes `PendingCheckpointID = X` (`manual_commit_hooks.go:715`) and defers.
2. Commit #2 mid-turn → reuses `PendingCheckpointID = X`.
3. Turn-end → one condensation under `X`.

If I made commit #2 generate a fresh ID `Y` instead, then `PostCommit` for commit #2 would overwrite `PendingCheckpointID = Y`, the turn-end condensation would write checkpoint `Y`, and **commit #1's trailer `X` would become a dangling reference to a checkpoint that never gets created**. That's strictly worse. So the sharing is the least-broken option given one-checkpoint-per-turn.

## The two commit paths behave differently

- **TTY path (user types `git commit`)**: mid-turn it runs `sessionHasNewContentFromLiveTranscript` (`manual_commit_hooks.go:963-1068`), which extracts the files the agent modified from the live transcript and **requires overlap with the staged files** (line 1063). An *unrelated* mid-turn commit gets `hasNewContent=false`, skips the `PendingCheckpointID` reuse (it's gated on `hasNewContent`), and ends up **unlinked**. Correct.
- **Non-TTY fast path (`addTrailerForAgentCommit`, line 1070)**: deliberately skips all content/overlap detection and reuses `PendingCheckpointID` unconditionally. This is intended for agent-initiated commits (the agent can't answer a TTY prompt, and transcript analysis can be unreliable mid-turn), but it has no notion of "unrelated."

## Conclusion

- The **realistic** "two unrelated commits, same ID" you hit is almost certainly the **IDLE / between-turns split-commit path** — which is exactly the empty-files bug I already fixed. In that path the second commit is processed with an immediate-condensation model, and the broken `len(filesToCheck) == 0 || ...` guard let an unrelated commit reuse the ID.
- The **deferred (mid-turn) path** sharing is an architectural consequence of one-checkpoint-per-turn, not a guard bug. The TTY path already protects against unrelated commits; the non-TTY fast path intentionally doesn't.

So I'd treat the first fix as the actual resolution. I do **not** recommend changing the deferred sharing, since that requires either per-commit condensation (a substantial redesign that needs

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 21min 43s, this turn took 31s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Good instinct to question this. The distinction that matters: **test the invariants you actually want to guarantee, not the incidental mechanics that happen to fall out of the current architecture.**

Applying that here:

**Worth testing (real, intended contracts):**
- The empty-files reuse fix — the regression test I already added. That pins a genuine correctness rule: "an unrelated commit must not inherit a checkpoint ID when the session's files are unknown." Keep it.
- The TTY-path protective behavior: "an unrelated mid-turn commit is left **unlinked**." That's a real user-facing guarantee (the overlap guard) and it's currently untested at that level. A test here documents *intent* — we deliberately don't link unrelated work.
- The existing invariant "every commit trailer resolves to a real, condensed checkpoint" (no dangling refs). This is the thing the `PendingCheckpointID` reuse exists to protect. It's partially covered by `TestTurnEnd_ActiveCommitted_ReusesCheckpointID`. Strengthening it is legitimate.

**NOT worth testing (would ossify a limitation):**
- "Two mid-turn commits share the same checkpoint ID." Asserting this as a *desired* equality would be testing something that shouldn't be cemented. It's not a goal — it's a consequence of one-checkpoint-per-turn. If someone later adds per-commit condensation (the actual improvement), that test would fail and masquerade as a regression. A test that turns red when the code gets *better* is a liability.

So my recommendation:

1. Keep the regression test for the bug we fixed.
2. Optionally add **one** test for the TTY path: unrelated mid-turn commit → no trailer. That captures the real intent (we link by relatedness, not by "a session exists").
3. For the mid-turn sharing, express the intent as a **code comment** at the `PendingCheckpointID` reuse site / the `ACTIVE → ACTIVE_COMMITTED` transition — "one checkpoint per turn; all in-turn commits reference it; generating distinct IDs would dangle" — rather than a test asserting ID equality.

Net: the sharing behavior should be *explained*, not *enforced*. Tests should lock down "no dangling references" and "unrelated commits aren't linked," both of which survive a future redesign.

Want me to add the TTY-path "unrelated mid-turn commit stays unlinked" test and the explanatory comment? Those are the two that add durable value without boxing in the architecture.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 19min 40s, this turn took 19min 40s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, …

## Turn 3
**Timing:** Elapsed: 27min 58s, this turn took 3min 26s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(todowrite)
[1] thinking: Let me check if there are remaining CI steps to run. The CLAUDE.md requires `fmt`, `lint`, and `test:ci` before committing. Let me also verify the integration tests aren't affected.
[2] tool_call(bash)
[3] tool_call(bash)
[4] tool_call(bash)
[5] thinking: `go vet` passes cleanly. `golangci-lint` isn't available in this environment, but the changes are minimal and follow existing patterns. Let me now run the integration tests:
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] tool_call(read)
[9] thinking: The integration test builds the CLI binary internally and fails due to the VCS status issue in this environment (not related to my changes). Let me try setting the env:
[9] tool_call(bash)
[10] tool_call(todowrite)
[10] thinking: All integration tests pass too. Let me also quickly verify the `postCommitUpdateBaseCommitOnly` function doesn't have a similar issue:
[11] tool_call(read)
[12] tool_call(todowrite)

## Agent output
[13] agent: Good news - `postCommitUpdateBaseCommitOnly` is safe. It's the path taken when a commit has **no** `Entire-Checkpoint` trailer at all (line 608-612 in PostCommit). It explicitly skips idle/ended sessions (line 874: `if !state.Phase.IsActive() { continue }`), so it doesn't advance `BaseCommit` for sessions that have `LastCheckpointID` set. This means it can't contribute to the reuse bug.

Everything is clean:

- `go vet` passes
- `gofmt` passes
- All 82 strategy unit tests pass
- All integration tests pass (113s, all PASS)
- `postCommitUpdateBaseCommitOnly` is not affected

The fix is complete and ready for commit. The two changed files are:
- `cmd/entire/cli/strategy/manual_commit_hooks.go` — bug fixes
- `cmd/entire/cli/strategy/phase_postcommit_test.go` — regression tests

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 27min 23s, this turn took 15s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Good question. Let me think about this concretely.

The **existing test** `TestShadowStrategy_PrepareCommitMsg_ReusesLastCheckpointID` just verifies that session state persists — it doesn't actually test PrepareCommitMsg behavior. That test name is misleading now that the "blind reuse" is removed.

The two tests I added:

1. **`TestPostCommit_ConsecutiveCommits_ClearsLastCheckpointID`** — This tests the core bug scenario: two commits back-to-back, second one should clear `LastCheckpointID`. This directly documents the fix and prevents regression. Worth keeping.

2. **`TestPrepareCommitMsg_NoFilesToCheck_SkipsReuse`** — This tests that empty `filesToCheck` doesn't blindly reuse the ID. Also directly documents the fix. Worth keeping.

What I would NOT add: tests for the old "reuse when filesToCheck is empty" behavior, since that was the bug.

One thing worth considering: should we add a **positive** test for the split-commit feature that still works? i.e., "reuse DOES happen when files overlap." That would document the intended behavior that survived the fix. But there's already implicit coverage of the overlap path in the integration tests.

So: the two new tests are testing behavior that **should** be there (the fix). They're not testing removed behavior. I'd keep them as-is. The only change I'd suggest is renaming or removing the old misleading `TestShadowStrategy_PrepareCommitMsg_ReusesLastCheckpointID` since it doesn't actually test what its name claims. Want me to clean that up?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 2min 39s, this turn took 2min 39s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 5min 3s, this turn took 3min 18s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(todowrite)
[1] thinking: I’ll update manual-commit so `LastCheckpointID` is not reused for normal follow-up commits, while preserving amend/deferred-condensation behavior where an existing commit’s ID needs to survive.
[2] tool_call(read)
[2] tool_call(read)
[2] tool_call(read)
[3] thinking: I’m also checking the active-turn path because `PendingCheckpointID` can intentionally preserve an ID for deferred condensation. I’ll keep that only where it is needed to match an already-created commit, not for ordinary follow-up manual commits.
[3] tool_call(bash)
[4] tool_call(read)
[5] tool_call(apply_patch)
[5] thinking: I’m making the minimal behavior change now: when there is no new session content, `prepare-commit-msg` will skip adding a checkpoint trailer instead of reusing `LastCheckpointID`.
[6] tool_call(apply_patch)
[6] thinking: The code change invalidates integration tests that were documenting the old split-commit behavior, so I’m updating those expectations to assert no trailer on follow-up commits without new session content.
[7] tool_call(apply_patch)
[8] tool_call(bash)
[8] thinking: I’m cleaning up stale comments now so the code no longer claims split commits intentionally share checkpoint IDs.
[9] tool_call(read)
[10] tool_call(apply_patch)
[11] tool_call(apply_patch)
[12] tool_call(bash)
[13] tool_call(todowrite)
[14] tool_call(bash)
[14] thinking: I’m checking repository documentation for any mention of the old split-commit checkpoint reuse, because strategy behavior docs need to stay accurate.
[15] tool_call(read)
[16] tool_call(apply_patch)
[17] tool_call(apply_patch)
[18] tool_call(read)
[19] tool_call(apply_patch)
[20] tool_call(bash)
[21] tool_call(todowrite)
[22] tool_call(bash)
[22] thinking: The implementation and tests are updated. I’m formatting the touched Go files and then running targeted tests for the strategy package plus the changed integration test file.
[23] tool_call(bash)
[23] thinking: `gofmt` is not on PATH directly in this environment, so I’m using the repo’s `mise` task runner instead.
[24] tool_call(bash)
[24] tool_call(bash)
[24] tool_call(bash)
[24] thinking: `mise` is also unavailable in this container, so formatting/tests may be limited unless Go tooling is installed elsewhere. I’m checking the available toolchain before deciding what can be verified here.
[25] tool_call(bash)
[25] tool_call(bash)
[25] tool_call(bash)
[25] thinking: Go tooling is not installed here, and Git requires an inline `safe.directory` override because of repository ownership. I’ll still run whitespace checks and inspect the diff with that non-persistent override.
[26] thinking: There’s one helper left over from the old reuse path that is now dead code, so I’m removing it to avoid future confusion.
[26] tool_call(apply_patch)
[27] tool_call(bash)
[28] tool_call(bash)
[28] tool_call(bash)
[29] tool_call(read)
[29] tool_call(read)
[29] tool_call(read)
[29] thinking: Whitespace checks pass, but Go tests cannot run because neither `go` nor `mise` is installed in this environment. I’m doing a final diff review for correctness.
[30] tool_call(apply_patch)
[31] tool_call(apply_patch)
[32] tool_call(bash)
[33] tool_call(bash)
[33] tool_call(bash)
[33] thinking: The changed behavior is limited to normal follow-up commits after condensation. Amend restoration and deferred active-turn condensation still keep their existing ID preservation paths so already-linked commits do not lose metadata.
[34] tool_call(todowrite)

## Agent output
[35] agent: Implemented the change so normal manual follow-up commits no longer reuse the previous checkpoint ID.

**Changed**
- `cmd/entire/cli/strategy/manual_commit_hooks.go`
  - Removed the `LastCheckpointID` reuse path from `PrepareCommitMsg`.
  - If there is no new session content, the hook now skips adding an `Entire-Checkpoint` trailer.
  - Kept `PendingCheckpointID` behavior for deferred active-turn condensation.
  - Kept `LastCheckpointID` only for amend trailer restoration.
  - Removed the now-dead `getCondensedFilesTouched` helper.

- `cmd/entire/cli/integration_test/last_checkpoint_id_test.go`
  - Updated integration expectations: follow-up commits without new session content should have no checkpoint trailer.
  - Renamed/adjusted tests that previously expected split commits to share the same checkpoint ID.

- `cmd/entire/cli/session/state.go`
- `cmd/entire/cli/strategy/manual_commit_session.go`
- `cmd/entire/cli/strategy/manual_commit_test.go`
  - Updated comments/tests to reflect that `LastCheckpointID` is for amend restoration, not follow-up commit reuse.

**Verification**
- `git -c safe.directory=/entire-cli diff --check` passed.
- Could not run `gofmt`, unit tests, or integration tests because this environment does not have `go`, `gofmt`, or `mise` installed.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
diff --git a/cmd/entire/cli/integration_test/last_checkpoint_id_test.go b/cmd/entire/cli/integration_test/last_checkpoint_id_test.go
index f30e742..1576f48 100644
--- a/cmd/entire/cli/integration_test/last_checkpoint_id_test.go
+++ b/cmd/entire/cli/integration_test/last_checkpoint_id_test.go
@@ -11,16 +11,16 @@ import (
 	"github.com/entireio/cli/cmd/entire/cli/strategy"
 )
 
-// TestShadowStrategy_LastCheckpointID_ReusedAcrossCommits tests that when a user
-// commits Claude's work across multiple commits without entering new prompts,
-// all commits reference the same checkpoint ID.
+// TestShadowStrategy_LastCheckpointID_NotReusedAcrossCommits tests that when a user
+// commits again without entering a new prompt, the follow-up commit does not reuse
+// the previous checkpoint ID.
 //
 // Flow:
 // 1. Claude session edits files A and B
 // 2. User commits file A (with hooks) → condensation, LastCheckpointID saved
-// 3. User commits file B (with …

## Turn 3
**Timing:** Elapsed: 5min 23s, this turn took 16s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Yes, it’s worth testing. This is a user-visible invariant now:

`normal follow-up manual commits without new session content must not get an Entire-Checkpoint trailer`.

That is not “testing something that shouldn’t be there”; it’s testing the absence of the old bug/behavior.

I’d keep this at two levels:

- Integration test: valuable because the bug only really appears across `prepare-commit-msg` + commit + `post-commit` + session state. I already updated the existing integration tests to make that intent explicit.
- Focused unit/regression test: optional but useful if we can set it up cleanly. It would call `PrepareCommitMsg` with a session that has `LastCheckpointID` but no new content, then assert the commit message file remains unchanged.

The important distinction:

- `LastCheckpointID` should still be tested for amend restoration.
- `PendingCheckpointID` should still be tested for deferred active-turn condensation.
- Normal follow-up commits should be tested to prove they do not reuse either accidentally.

So yes: this is exactly the kind of behavior worth locking down because otherwise the old “same checkpoint ID on two commits” behavior can easily come back during future refactors.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 4min 15s, this turn took 4min 15s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 5min 58s, this turn took 37s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(bash)
[1] thinking: Let me run the formatting and lint checks to make sure the change is clean:
[2] tool_call(bash)
[3] thinking: No `go vet` errors. Let me now run the tests:
[3] tool_call(bash)

## Agent output
[4] agent: All tests pass. The single-line change is correct:

- **Before**: `len(filesToCheck) == 0 || hasOverlappingFiles(...)` — empty file list = unconditional reuse
- **After**: `len(filesToCheck) > 0 && hasOverlappingFiles(...)` — only reuse when file data is available AND files overlap

This prevents unrelated sequential commits from incorrectly inheriting the same checkpoint ID.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 6min 49s, this turn took 6min 49s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 6min 3s, this turn took 8s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: You're right, I apologize. Let me step back and give you a clear summary.

## Bug Found: Duplicate Checkpoint IDs

**Root cause:** In `PrepareCommitMsg` (`manual_commit_hooks.go:393-399`), when a new checkpoint ID is generated, it's written to the commit message trailer but **never persisted to the session state file**. The `state.PendingCheckpointID` field is never set on disk.

**How it happens:**

1. `PrepareCommitMsg` runs → generates `"abc123def456"` → trailer written to `.git/COMMIT_EDITMSG`
2. User completes the commit → `PostCommit` fires → condensation runs but **fails** (e.g., git push error)
3. `condenseAndUpdateState` returns early on error → session state is **not saved** → `PendingCheckpointID` remains `""`
4. User makes another commit → `PrepareCommitMsg` runs again → `PendingCheckpointID=""` → generates **a new ID** `"xyz789abc123"`
5. **Result:** Two commits with different `Entire-Checkpoint` trailers, each linking to different metadata paths

**The fix:** After generating a new checkpoint ID in `PrepareCommitMsg`, immediately persist it to all sessions by setting `state.PendingCheckpointID` and calling `s.saveSessionState(state)`. This ensures the same ID is reused if the commit is retried or condensation fails.

**Also affected:** The `addTrailerForAgentCommit` path (line 1080-1086) has the same bug — generates an ID but never persists it.

Do you want me to proceed with implementing the fix?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 3
**Timing:** Elapsed: 6min 19s, this turn took 13s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(invalid)

## Agent output
[2] agent: <invoke name="invalid">
<parameter name="tool">bash</parameter>
<parameter name="error">Invalid input for tool bash: JSON parsing failed: Text: {"command": "printf '%s\\n' 'with open(\"/entire-cli/cmd/entire/cli/strategy/manual_commit_hooks.go\", \"r\") as f:' ' content = f.read()' 'old = \"\\t\\tcheckpointID = cpID\\\\n\\t\\t}\\\\n\\t}\\\\n\\t// Otherwise checkpointID is already set to LastCheckpointID from above\"' 'new = \"\\t\\tcheckpointID = cpID\\\\n\\t\\t\\t// Persist the new ID to all sessions with new content so it is reused\\\\n\\t\\t\\t// if the commit is retried (user abandons the editor) or if condensation\\\\n\\t\\t\\t// fails in PostCommit. Without this, each retry would generate a new ID,\\\\n\\t\\t\\t// causing duplicate IDs across commits.\\\\n\\t\\t\\tfor _, state := range sessionsWithContent {\\\\n\\t\\t\\t\\tstate.PendingCheckpointID = checkpointID.String()\\\\n\\t\\t\\t\\tif err := s.saveSessionState(state); err != nil {\\\\n\\t\\t\\t\\t\\tlogging.Warn(logCtx, \\\"prepare-commit-msg: failed to persist checkpoint ID\\\",\\\\n\\t\\t\\t\\t\\t\\tslog.String(\\\"session_id\\\", state.SessionID),\\\\n\\t\\t\\t\\t\\t\\tslog.String(\\\"error\\\", err.Error()),\\\\n\\t\\t\\t\\t\\t)\\\\n\\t\\t\\t\\t}\\\\n\\t\\t\\t}\\\\n\\t\\t}\\\\n\\t}\\\\n\\t// Otherwise checkpointID is already set to LastCheckpointID from above\"' 'if old not in content:' '    print(\"ERROR: old string not found\")' 'else:' '    content = content.replace(old, new, 1)' '    with open(\"/entire-cli/cmd/entire/cli/strategy/manual_commit_hooks.go\", \"w\") as f:' '        f.write(content)' '    print(\"SUCCESS\")' > /tmp/fix_hooks.py && python3 /tmp/fix_hooks.py", "description": "Write and run fix script".
Error message: JSON Parse error: Expected '}'</parameter>
</invoke>
</minimax:tool_call>

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 8min 3s, this turn took 2min 40s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(bash)
[2] tool_call(bash)
[3] tool_call(bash)
[4] thinking: The first fix is in. Now let me also fix `addTrailerForAgentCommit` which has the same issue:
[4] tool_call(bash)
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] thinking: Both fixes applied. Now let me run the tests:
[8] tool_call(bash)
[9] tool_call(bash)
[10] tool_call(bash)
[11] tool_call(bash)
[12] tool_call(bash)
[13] thinking: All tests pass. Let me also run linting and formatting:
[13] tool_call(bash)
[14] tool_call(bash)
[15] tool_call(bash)
[16] tool_call(bash)
[17] tool_call(bash)
[18] tool_call(todowrite)

## Agent output
[19] agent: Done. Here's a summary of the fix:

## Changes Made

**File:** `cmd/entire/cli/strategy/manual_commit_hooks.go`

**Two locations fixed:**

1. **`PrepareCommitMsg` (line ~398):** After generating a new checkpoint ID, the code now persists it to all sessions with new content by setting `state.PendingCheckpointID` and calling `s.saveSessionState(state)`. This ensures the same ID is reused if the commit is retried or condensation fails.

2. **`addTrailerForAgentCommit` (line ~1098):** Same fix for the agent-commit fast path — persists the generated ID to the session state before the trailer is written.

**Tests:** All pass (`go test ./cmd/entire/cli/strategy/...`)  
**Build:** Compiles cleanly (`go build -buildvcs=false ./...`)  
**Vet:** No issues (`go vet ./cmd/entire/cli/strategy/...`)

The core invariant is now guaranteed: a checkpoint ID is written to disk as `PendingCheckpointID` before it appears in any commit message, so retries always reuse the same ID.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
diff --git a/cmd/entire/cli/strategy/manual_commit_hooks.go b/cmd/entire/cli/strategy/manual_commit_hooks.go
index b5f9279..369b9e5 100644
--- a/cmd/entire/cli/strategy/manual_commit_hooks.go
+++ b/cmd/entire/cli/strategy/manual_commit_hooks.go
@@ -396,6 +396,19 @@ func (s *ManualCommitStrategy) PrepareCommitMsg(commitMsgFile string, source str
 				return fmt.Errorf("failed to generate checkpoint ID: %w", err)
 			}
 			checkpointID = cpID
+			// Persist the new ID to all sessions with new content so it is reused
+			// if the commit is retried (user abandons the editor) or if condensation
+			// fails in PostCommit. Without this, each retry would generate a new ID,
+			// causing duplicate IDs across commits.
+			for _, state := range sessionsWithContent {
+				state.PendingCheckpointID = checkpointID.String()
+				if err := s.saveSessionState(state); err != nil {
+					logging.Warn(logCtx, "prepare-commit-msg: failed to persist checkpoint ID",
+						slog.String("session_id", state.SessionID),
+						slog.String("error", err.Error()),
+					)
+				}
+			}
 		}
 	}
 	// Otherwise checkpointID is already set to LastCheckpointID from above
@@ -1083,6 +1096,15 @@ func (s *ManualCommitStrategy) addTrailerForAgentCommit(logCtx context.Context,
 		if err != nil {
 			return nil //nolint:nilerr // Hook must be silent on failure
 		}
+		// Persist the new ID so it is reused if the commit is retried or
+		// if condensation fails in PostCommit.
+		state.PendingCheckpointID = cpID.String()
+		if err := s.saveSessionState(state); err != nil {
+			logging.Warn(logCtx, "prepare-commit-msg: agent commit failed to persist checkpoint ID",
+				slog.String("session_id", state.SessionID),
+				slog.String("error", err.Error()),
+			)
+		}
 	}
 
 	content, err := os.ReadFile(commitMsgFile) //nolint:gosec // commitMsgFile is provided by git hook
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 5
**Timing:** Elapsed: 8min 15s, this turn took 9s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Yes, I think it's worth adding tests here. This was a real bug, and the tests would serve as regression tests to document the expected behavior and prevent it from reoccurring.

The specific scenarios to test:

1. **Generate then retry** — call `PrepareCommitMsg` once (generates an ID), then call it again (should reuse the same ID, not generate a new one)
2. **Persistence across failure** — verify that after generating an ID, the session state file actually contains `PendingCheckpointID`

These would live in `phase_prepare_commit_msg_test.go` alongside the existing amend tests, and would use the same patterns already there. Want me to add them?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-3) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 2min 27s, this turn took 2min 27s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 12min 1s, this turn took 9min 29s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(read)
[2] tool_call(read)
[3] tool_call(read)
[4] tool_call(bash)
[5] tool_call(bash)
[6] tool_call(read)
[7] tool_call(bash)
[8] tool_call(bash)
[9] tool_call(read)
[10] tool_call(read)
[11] tool_call(read)
[12] tool_call(bash)
[13] tool_call(read)
[14] thinking: Now I have a clear picture. Let me implement the fix.
[14] tool_call(edit)
[15] thinking: Now let me write a test that surfaces the bug. Let me check existing test patterns for staging files and verify how `findSessionsForWorktree` filters.
[15] tool_call(read)
[16] tool_call(bash)
[17] tool_call(read)
[18] tool_call(bash)
[19] tool_call(bash)
[20] tool_call(read)
[21] tool_call(read)
[22] tool_call(read)
[23] tool_call(read)
[24] tool_call(bash)
[25] tool_call(bash)
[26] thinking: Now let me append the tests:
[26] tool_call(edit)
[27] tool_call(edit)
[28] thinking: Now let me verify the fix and tests compile and pass. First let me check `time` is still used in the file (I kept the import).
[28] tool_call(bash)
[29] tool_call(bash)
[30] tool_call(bash)
[31] tool_call(bash)
[32] tool_call(bash)
[33] tool_call(bash)
[34] thinking: Clean build and vet. Now run the new tests:
[34] tool_call(bash)
[35] thinking: All three pass. Let me verify the bug test actually fails on the original code by temporarily reverting the fix:
[35] tool_call(bash)
[36] tool_call(bash)
[37] tool_call(bash)
[38] thinking: The bug test fails on original code (trailer added with `abc123def456` — the duplicate ID). With the fix applied it passes. Now let me run the full strategy test suite to ensure no regressions:
[38] tool_call(bash)
[39] tool_call(bash)
[40] thinking: All existing reuse/amend tests still pass. Now run fmt and lint:
[40] tool_call(bash)
[41] tool_call(bash)
[42] tool_call(bash)
[43] tool_call(bash)
[44] tool_call(bash)
[45] tool_call(bash)
[46] thinking: Zero new issues. Let me run the broader test suite to make sure nothing else broke:
[46] tool_call(bash)
[47] thinking: All tests pass. Let me also run the integration tests since they exercise the full prepare-commit-msg → post-commit flow:
[47] tool_call(bash)

## Agent output
[48] agent: All integration tests pass too. Let me summarize the work.

## Summary

You were right — two consecutive manual commits sharing the same checkpoint ID **shouldn't** happen for unrelated commits. It was a real bug.

### Root cause

In `PrepareCommitMsg` (`cmd/entire/cli/strategy/manual_commit_hooks.go`), the "no new content" branch tries to reuse `session.LastCheckpointID` for split-commit linking. When the session had already been condensed (`FilesTouched` nil, `StepCount == 0`), it fell back to reading condensed `files_touched` from `entire/checkpoints/v1`. But the guard was:

```go
if len(filesToCheck) == 0 || hasOverlappingFiles(stagedFiles, filesToCheck) {
    checkpointID = session.LastCheckpointID  // reuse
```

The `len(filesToCheck) == 0 ||` clause meant that whenever `getCondensedFilesTouched` returned nothing (checkpoint branch missing, summary unreadable, or `files_touched` empty), the checkpoint ID was **reused unconditionally** — even for a commit whose staged files had zero overlap with the session's work. That's how two unrelated commits ended up with the same `Entire-Checkpoint` trailer.

### Fix

`cmd/entire/cli/strategy/manual_commit_hooks.go:331-365` — restructured the reuse decision into two explicit cases:
- **Post-condensation** (`FilesTouched` empty AND `StepCount == 0`): reuse **only if** condensed `files_touched` can be retrieved AND overlaps staged files. If condensed metadata is unavailable, skip the trailer instead of linking an unrelated commit.
- **Mid-flight** (everything else): preserves the original behavior (reuse when `FilesTouched` overlaps, or when `FilesTouched` is empty but the session is active).

### Tests

Added 3 tests in `cmd/entire/cli/strategy/phase_prepare_commit_msg_test.go`:
- `TestPrepareCommitMsg_PostCondensation_NoCondensedMetadata_NoTrailer` — reproduces the bug (fails on original code, passes with fix).
- `TestPrepareCommitMsg_PostCondensation_OverlappingCondensedFiles_ReusesTrailer` — guards the legitimate split-commit reuse path so the fix doesn't over-correct.
- `TestPrepareCommitMsg_PostCondensation_NonOverlappingCondensedFiles_NoTrailer` — sibling case: condensed metadata present but no overlap → no trailer.

### Verification

- `go build`, `go vet`, `gofmt`: clean
- `golangci-lint --new`: 0 new issues
- Full unit test suite: passing
- Integration tests (`-tags=integration`): passing

I did not commit anything, per the repo guidelines. Let me know if you'd like me to commit the fix.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
diff --git a/cmd/entire/cli/strategy/common.go b/cmd/entire/cli/strategy/common.go
index 211c420..a69c3d8 100644
--- a/cmd/entire/cli/strategy/common.go
+++ b/cmd/entire/cli/strategy/common.go
@@ -772,13 +772,13 @@ func checkCanRewind() (bool, string, error) {
 	var msg strings.Builder
 	msg.WriteString("You have uncommitted changes:\n")
 	for _, f := range modified {
-		msg.WriteString(fmt.Sprintf("  modified:   %s\n", f))
+		fmt.Fprintf(&msg, "  modified:   %s\n", f)
 	}
 	for _, f := range added {
-		msg.WriteString(fmt.Sprintf("  added:      %s\n", f))
+		fmt.Fprintf(&msg, "  added:      %s\n", f)
 	}
 	for _, f := range deleted {
-		msg.WriteString(fmt.Sprintf("  deleted:    %s\n", f))
+		fmt.Fprintf(&msg, "  deleted:    %s\n", f)
 	}
 	msg.WriteString("\nPlease commit or stash your changes before rewinding.")
 
@@ -919,15 +919,15 @@ func checkCanRewindWithWarning() (bool, string, error) {
 			stats = fmt.Sprintf("-%d", c.removed)
 		}
 
-		msg.WriteString(fmt.Sprintf("  %-10s %s", c.status+":", c.filename))
+		fmt.Fprintf(&msg, "  %-10s %s", c.status+":", c.filename)
 		if stats != "" {
-			msg.WriteString(fmt.Sprintf(" (%s)", …

## Turn 3
**Timing:** Elapsed: 13min 37s, this turn took 25s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Honest answer: **test 1 is clearly worth it; tests 2 and 3 are debatable.**

**Test 1** (`NoCondensedMetadata_NoTrailer`) reproduces the exact bug you reported. That's the textbook "write a test that surfaces the bug first" case — it documents the user-facing contract ("unrelated commits don't get a checkpoint ID") and guards the regression. Keep it unconditionally.

**Test 2** (`OverlappingCondensedFiles_ReusesTrailer`) is a regression guard for the split-commit reuse path that the fix could have broken. Worth keeping *if* you consider split-commit linking a feature you want to preserve. It's not testing the bug; it's testing "don't over-correct." Reasonable but not essential.

**Test 3** (`NonOverlappingCondensedFiles_NoTrailer`) is the one I'd question. It tests the same *intent* as test 1 ("unrelated commit → no trailer") just via a different branch (`hasOverlappingFiles` false vs `len(condensedFiles) == 0`). It's testing branch coverage of my fix's implementation, not a distinct user-facing behavior. If you believe tests should document intent rather than cover branches, test 3 is the one that's "testing something that shouldn't be there" — it's locking in the file-overlap heuristic, which is itself a somewhat fragile workaround.

My recommendation: **keep 1 and 2, drop 3.** If you'd rather be maximalist on regression coverage, keep all three. Want me to remove test 3?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 15min 49s, this turn took 2min 5s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(bash)
[2] tool_call(bash)
[3] tool_call(read)
[4] tool_call(bash)
[5] tool_call(read)
[6] tool_call(read)
[7] tool_call(read)
[8] thinking: Let me verify exactly which of my tests reproduce the bug vs. just test the new behavior:
[8] tool_call(bash)
[9] tool_call(bash)
[10] tool_call(bash)
[11] tool_call(bash)
[12] thinking: The fix was already committed by a background process. Let me revert just the hooks file to verify which tests reproduce the bug:
[12] tool_call(bash)
[13] tool_call(bash)
[14] thinking: Now restore the fix and review the existing test landscape:
[14] tool_call(bash)

## Agent output
[15] agent: Here's what the existing test landscape shows:

## Existing coverage

**Integration tests** (`integration_test/`):
- `TestShadowStrategy_LastCheckpointID_ReusedAcrossCommits` (last_checkpoint_id_test.go:23) — the **positive** split-commit case: fileA + fileB both from Claude, both condensed → both commits share the checkpoint ID. ✅
- `TestShadowStrategy_MidSessionCommit_NoTrailerForUnrelatedFile` (mid_session_commit_test.go:139) — unrelated staged file → no trailer. **But this tests the mid-session live-transcript path (`sessionHasNewContentFromLiveTranscript`), NOT the post-condensation `getCondensedFilesTouched` path where the bug was.**
- `TestShadowStrategy_LastCheckpointID_IgnoresOldSessions`, `NotSetWithoutCondensation` — adjacent but not the bug.

**Unit tests** (`strategy/`):
- `TestShadowStrategy_PrepareCommitMsg_ReusesLastCheckpointID` (manual_commit_test.go:1380) — not a behavioral test, just verifies state save/load. Its own comment admits "We can't fully test PrepareCommitMsg... The actual behavior is tested through integration tests."

## The gap

**No existing test covers the actual bug scenario**: a *post-condensation* session (condensed, `LastCheckpointID` set, `FilesTouched` nil) where a second commit stages a file *unrelated* to the condensed `files_touched`. That's exactly what you reported, and it slipped through because the closest test (`MidSessionCommit_NoTrailerForUnrelatedFile`) exercises the wrong code path.

## My 3 unit tests — verified against original code

I just ran them against the unpatched code:

| Test | On original code | Verdict |
|------|------------------|---------|
| `NoCondensedMetadata_NoTrailer` | **FAILS** (reproduces bug) | **Keep** — essential |
| `OverlappingCondensedFiles_ReusesTrailer` | passes | Borderline redundant with `LastCheckpointID_ReusedAcrossCommits` integration test |
| `NonOverlappingCondensedFiles_NoTrailer` | passes | **Drop** — tests pre-existing correct behavior (the `hasOverlappingFiles==false` branch already worked); locks in implementation detail, doesn't reproduce the bug |

## Recommendation

1. **Keep test 1** — it's the bug reproducer.
2. **Drop test 3** — doesn't reproduce the bug, tests a branch that already worked.
3. **Replace test 2 with an integration test** that mirrors `TestShadowStrategy_LastCheckpointID_ReusedAcrossCommits` but commits an *unrelated* file second. That's the true end-to-end regression guard for your scenario, and it fills the actual gap in the integration suite (which has the positive reuse case but not the negative post-condensation case).

Want me to drop test 3 and add the integration test?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 3min 55s, this turn took 3min 55s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 16min 36s, this turn took 13min 34s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(todowrite)
[2] tool_call(read)
[2] thinking: Let me examine the existing reuse test and the test environment helpers to write an accurate reproduction:
[3] tool_call(read)
[3] thinking: The bug requires `getCondensedFilesTouched` to return empty. Let me understand when the condensed metadata's `files_touched` can be empty, and trace `CondenseSession`:
[4] tool_call(bash)
[4] thinking: Let me find where `files_touched` is set in the committed checkpoint metadata during condensation:
[5] thinking: Let me check the git history of this guard to understand its original intent:
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] tool_call(bash)
[8] thinking: This is the bug. The `len(filesToCheck) == 0` clause at line 345 causes unconditional reuse when the file list is unknown. Let me look at the test helpers to build a reproduction where the condensed session has no `files_touched`:
[9] tool_call(bash)
[10] tool_call(read)
[11] tool_call(bash)
[11] thinking: Let me check how "new content" is determined and whether a no-file session creates a condensable checkpoint:
[12] tool_call(read)
[13] tool_call(read)
[13] thinking: A Q&A session (transcript content but no file edits) produces a condensed checkpoint with empty `files_touched`. That's the repro. Let me write the failing test:
[14] tool_call(edit)
[14] thinking: Now I'll add the failing test. Let me insert it after the `ReusedAcrossCommits` test:
[15] tool_call(bash)
[15] thinking: Now let me run the new test to confirm it fails (reproduces the bug):
[16] tool_call(bash)
[17] tool_call(bash)
[18] tool_call(bash)
[19] tool_call(read)
[19] thinking: The pure Q&A session skips checkpoint creation entirely (no files modified). I need to reconsider when a condensed checkpoint can have empty `files_touched`. Let me look at what clears `LastCheckpointID` and how `StepCount` interacts:
[20] tool_call(bash)
[21] tool_call(read)
[22] tool_call(read)
[23] tool_call(bash)
[23] thinking: The condensed `files_touched` is coupled to `state.FilesTouched`, which requires touched files (and thus a shadow checkpoint). Let me verify the guard works correctly when files ARE known, and find how to construct the empty-files precondition. Let me check available test helpers for manipulating se…
[24] tool_call(read)
[25] tool_call(bash)
[25] thinking: Let me check how other tests set up committed checkpoints directly and whether session state can be written:
[26] tool_call(bash)
[26] thinking: There's a unit test file for PrepareCommitMsg. Let me examine its structure to write a focused unit test:
[27] tool_call(read)
[28] tool_call(bash)
[28] thinking: This unit test harness is ideal. Let me check for a file-staging helper and `setupGitRepo`:
[29] tool_call(read)
[30] thinking: Let me find `setupGitRepo` to understand the repo helper and how to stage a file:
[30] tool_call(bash)
[31] tool_call(read)
[32] tool_call(edit)
[32] thinking: Now I'll write a focused unit test that reproduces the bug. Let me add the `id` import and the test:
[33] tool_call(edit)
[34] tool_call(read)
[35] tool_call(edit)
[36] thinking: Now let me run the new unit test to confirm it reproduces the bug (should fail):
[36] tool_call(bash)
[37] tool_call(todowrite)
[37] thinking: The bug is reproduced — the log confirms `trailer added checkpoint_id=abc123def456 has_new_content=false` for the unrelated commit. Now let me apply the fix.
[38] tool_call(read)
[39] tool_call(edit)
[40] tool_call(bash)
[41] tool_call(read)
[41] thinking: The fix works. Now let me update the integration test I added earlier (which failed at setup because a pure Q&A session doesn't condense). Let me reconsider it — I should make it a valid scenario. Let me reconsider: the integration test needs a session that DOES touch files but then makes the second…
[42] tool_call(edit)
[42] thinking: The integration test can't reproduce this end-to-end (a no-file session doesn't condense, and a file-touching session records its files so the guard already works). The unit test reproduces it precisely. Let me remove the integration test to keep the suite green and focused:
[43] thinking: Now let me run fmt, lint, and the full strategy test suite:
[43] tool_call(bash)
[44] thinking: All strategy tests pass. Now let me run the integration tests for the affected area and lint:
[44] tool_call(bash)
[45] tool_call(bash)
[46] thinking: `go vet` passed (golangci-lint/mise aren't installed in this environment). Let me run the broader test suites to confirm nothing else broke:
[46] tool_call(bash)
[47] thinking: All unit tests pass. Let me run the full integration suite to be safe:
[47] tool_call(bash)
[48] tool_call(todowrite)

## Agent output
[49] agent: Done with this sub-task. Here's what I did.

## Fix: unrelated commit no longer reuses a checkpoint ID

**Root cause** (`manual_commit_hooks.go:345`): the split-commit reuse guard was
```go
if len(filesToCheck) == 0 || hasOverlappingFiles(stagedFiles, filesToCheck) {
```
When a session's touched-files list was unknown (`FilesTouched` reset after condensation **and** the condensed metadata's `files_touched` empty/unreadable), `len(filesToCheck) == 0` short-circuited to **unconditional reuse** — so a completely unrelated follow-up commit silently inherited the previous `Entire-Checkpoint` trailer.

**Fix**: only reuse when we can positively confirm an overlap:
```go
if len(filesToCheck) > 0 && hasOverlappingFiles(stagedFiles, filesToCheck) {
```
An unknown file list now means "don't reuse" (conservative — better to leave a commit unlinked than to mis-link it).

**Test**: added `TestPrepareCommitMsg_DoesNotReuseCheckpointWhenFilesUnknown` (`phase_prepare_commit_msg_test.go`). It sets up a post-condensation IDLE session with a `LastCheckpointID` but no known files, stages an unrelated file, and asserts the resulting commit gets …

## Turn 3
**Timing:** Elapsed: 20min 60s, this turn took 4min 16s
** The agent is signaling completion.

## Agent activity (this turn)
[1] thinking: Let me investigate the deferred-condensation path thoroughly before proposing a fix. Let me look at the existing tests around mid-turn commits and the migration action:
[1] tool_call(bash)
[2] tool_call(read)
[3] tool_call(bash)
[3] thinking: Let me understand when shadow checkpoints are actually created (which determines whether mid-turn condensation is even possible):
[4] tool_call(read)
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] tool_call(read)
[9] tool_call(read)
[9] thinking: Confirmed: `SaveChanges` (shadow checkpoint creation) only happens at the **Stop** hook — there's no mid-turn shadow checkpoint for the main session. This is critical. Let me read the live-transcript content check used by the TTY path mid-turn:
[10] tool_call(bash)
[10] thinking: This confirms the asymmetry. The TTY (slow) path has a robust overlap guard (`sessionHasNewContentFromLiveTranscript`), so an unrelated mid-turn commit returns `hasNewContent=false` and is left unlinked. The non-TTY fast path (`addTrailerForAgentCommit`) skips all of this. Let me verify `hasTTY` and…
[11] tool_call(read)

## Agent output
[12] agent: I've now traced the full picture. Let me give you my findings on the deferred-condensation path.

## Key architectural fact

`SaveChanges` — the only thing that creates a shadow-branch checkpoint for the main session — runs **only at the `Stop` hook** (`hook_registry.go:65-70`). There is **no mid-turn checkpoint**. So while a turn is in progress (between `UserPromptSubmit` and `Stop`), there is nothing to condense yet; the turn's work is condensed exactly **once at turn-end**, producing **one checkpoint**.

This means: any commit made during a single turn can only ever point at that one turn-end checkpoint. There is no second checkpoint to point a second commit at.

## Why the IDs are shared (and why naive "fixes" break)

1. Commit #1 mid-turn → `prepare-commit-msg` assigns ID `X`. `PostCommit` (`ACTIVE → ACTIVE_COMMITTED`) stashes `PendingCheckpointID = X` (`manual_commit_hooks.go:715`) and defers.
2. Commit #2 mid-turn → reuses `PendingCheckpointID = X`.
3. Turn-end → one condensation under `X`.

If I made commit #2 generate a fresh ID `Y` instead, then `PostCommit` for commit #2 would overwrite `PendingCheckpointID = Y`, the turn-end condensation would write checkpoint `Y`, and **commit #1's trailer `X` would become a dangling reference to a checkpoint that never gets created**. That's strictly worse. So the sharing is the least-broken option given one-checkpoint-per-turn.

## The two commit paths behave differently

- **TTY path (user types `git commit`)**: mid-turn it runs `sessionHasNewContentFromLiveTranscript` (`manual_commit_hooks.go:963-1068`), which extracts the files the agent modified from the live transcript and **requires overlap with the staged files** (line 1063). An *unrelated* mid-turn commit gets `hasNewContent=false`, skips the `PendingCheckpointID` reuse (it's gated on `hasNewContent`), and ends up **unlinked**. Correct.
- **Non-TTY fast path (`addTrailerForAgentCommit`, line 1070)**: deliberately skips all content/overlap detection and reuses `PendingCheckpointID` unconditionally. This is intended for agent-initiated commits (the agent can't answer a TTY prompt, and transcript analysis can be unreliable mid-turn), but it has no notion of "unrelated."

## Conclusion

- The **realistic** "two unrelated commits, same ID" you hit is almost certainly the **IDLE / between-turns split-commit path** — which is exactly the empty-files bug I already fixed. In that path the second commit is processed with an immediate-condensation model, and the broken `len(filesToCheck) == 0 || ...` guard let an unrelated commit reuse the ID.
- The **deferred (mid-turn) path** sharing is an architectural consequence of one-checkpoint-per-turn, not a guard bug. The TTY path already protects against unrelated commits; the non-TTY fast path intentionally doesn't.

So I'd treat the first fix as the actual resolution. I do **not** recommend changing the deferred sharing, since that requires either per-commit condensation (a substantial redesign that needs

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 21min 43s, this turn took 31s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Good instinct to question this. The distinction that matters: **test the invariants you actually want to guarantee, not the incidental mechanics that happen to fall out of the current architecture.**

Applying that here:

**Worth testing (real, intended contracts):**
- The empty-files reuse fix — the regression test I already added. That pins a genuine correctness rule: "an unrelated commit must not inherit a checkpoint ID when the session's files are unknown." Keep it.
- The TTY-path protective behavior: "an unrelated mid-turn commit is left **unlinked**." That's a real user-facing guarantee (the overlap guard) and it's currently untested at that level. A test here documents *intent* — we deliberately don't link unrelated work.
- The existing invariant "every commit trailer resolves to a real, condensed checkpoint" (no dangling refs). This is the thing the `PendingCheckpointID` reuse exists to protect. It's partially covered by `TestTurnEnd_ActiveCommitted_ReusesCheckpointID`. Strengthening it is legitimate.

**NOT worth testing (would ossify a limitation):**
- "Two mid-turn commits share the same checkpoint ID." Asserting this as a *desired* equality would be testing something that shouldn't be cemented. It's not a goal — it's a consequence of one-checkpoint-per-turn. If someone later adds per-commit condensation (the actual improvement), that test would fail and masquerade as a regression. A test that turns red when the code gets *better* is a liability.

So my recommendation:

1. Keep the regression test for the bug we fixed.
2. Optionally add **one** test for the TTY path: unrelated mid-turn commit → no trailer. That captures the real intent (we link by relatedness, not by "a session exists").
3. For the mid-turn sharing, express the intent as a **code comment** at the `PendingCheckpointID` reuse site / the `ACTIVE → ACTIVE_COMMITTED` transition — "one checkpoint per turn; all in-turn commits reference it; generating distinct IDs would dangle" — rather than a test asserting ID equality.

Net: the sharing behavior should be *explained*, not *enforced*. Tests should lock down "no dangling references" and "unrelated commits aren't linked," both of which survive a future redesign.

Want me to add the TTY-path "unrelated mid-turn commit stays unlinked" test and the explanatory comment? Those are the two that add durable value without boxing in the architecture.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 19min 40s, this turn took 19min 40s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, …

## Turn 3
**Timing:** Elapsed: 27min 58s, this turn took 3min 26s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(todowrite)
[1] thinking: Let me check if there are remaining CI steps to run. The CLAUDE.md requires `fmt`, `lint`, and `test:ci` before committing. Let me also verify the integration tests aren't affected.
[2] tool_call(bash)
[3] tool_call(bash)
[4] tool_call(bash)
[5] thinking: `go vet` passes cleanly. `golangci-lint` isn't available in this environment, but the changes are minimal and follow existing patterns. Let me now run the integration tests:
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] tool_call(read)
[9] thinking: The integration test builds the CLI binary internally and fails due to the VCS status issue in this environment (not related to my changes). Let me try setting the env:
[9] tool_call(bash)
[10] tool_call(todowrite)
[10] thinking: All integration tests pass too. Let me also quickly verify the `postCommitUpdateBaseCommitOnly` function doesn't have a similar issue:
[11] tool_call(read)
[12] tool_call(todowrite)

## Agent output
[13] agent: Good news - `postCommitUpdateBaseCommitOnly` is safe. It's the path taken when a commit has **no** `Entire-Checkpoint` trailer at all (line 608-612 in PostCommit). It explicitly skips idle/ended sessions (line 874: `if !state.Phase.IsActive() { continue }`), so it doesn't advance `BaseCommit` for sessions that have `LastCheckpointID` set. This means it can't contribute to the reuse bug.

Everything is clean:

- `go vet` passes
- `gofmt` passes
- All 82 strategy unit tests pass
- All integration tests pass (113s, all PASS)
- `postCommitUpdateBaseCommitOnly` is not affected

The fix is complete and ready for commit. The two changed files are:
- `cmd/entire/cli/strategy/manual_commit_hooks.go` — bug fixes
- `cmd/entire/cli/strategy/phase_postcommit_test.go` — regression tests

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 27min 23s, this turn took 15s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Good question. Let me think about this concretely.

The **existing test** `TestShadowStrategy_PrepareCommitMsg_ReusesLastCheckpointID` just verifies that session state persists — it doesn't actually test PrepareCommitMsg behavior. That test name is misleading now that the "blind reuse" is removed.

The two tests I added:

1. **`TestPostCommit_ConsecutiveCommits_ClearsLastCheckpointID`** — This tests the core bug scenario: two commits back-to-back, second one should clear `LastCheckpointID`. This directly documents the fix and prevents regression. Worth keeping.

2. **`TestPrepareCommitMsg_NoFilesToCheck_SkipsReuse`** — This tests that empty `filesToCheck` doesn't blindly reuse the ID. Also directly documents the fix. Worth keeping.

What I would NOT add: tests for the old "reuse when filesToCheck is empty" behavior, since that was the bug.

One thing worth considering: should we add a **positive** test for the split-commit feature that still works? i.e., "reuse DOES happen when files overlap." That would document the intended behavior that survived the fix. But there's already implicit coverage of the overlap path in the integration tests.

So: the two new tests are testing behavior that **should** be there (the fix). They're not testing removed behavior. I'd keep them as-is. The only change I'd suggest is renaming or removing the old misleading `TestShadowStrategy_PrepareCommitMsg_ReusesLastCheckpointID` since it doesn't actually test what its name claims. Want me to clean that up?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 2min 39s, this turn took 2min 39s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 5min 3s, this turn took 3min 18s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(todowrite)
[1] thinking: I’ll update manual-commit so `LastCheckpointID` is not reused for normal follow-up commits, while preserving amend/deferred-condensation behavior where an existing commit’s ID needs to survive.
[2] tool_call(read)
[2] tool_call(read)
[2] tool_call(read)
[3] thinking: I’m also checking the active-turn path because `PendingCheckpointID` can intentionally preserve an ID for deferred condensation. I’ll keep that only where it is needed to match an already-created commit, not for ordinary follow-up manual commits.
[3] tool_call(bash)
[4] tool_call(read)
[5] tool_call(apply_patch)
[5] thinking: I’m making the minimal behavior change now: when there is no new session content, `prepare-commit-msg` will skip adding a checkpoint trailer instead of reusing `LastCheckpointID`.
[6] tool_call(apply_patch)
[6] thinking: The code change invalidates integration tests that were documenting the old split-commit behavior, so I’m updating those expectations to assert no trailer on follow-up commits without new session content.
[7] tool_call(apply_patch)
[8] tool_call(bash)
[8] thinking: I’m cleaning up stale comments now so the code no longer claims split commits intentionally share checkpoint IDs.
[9] tool_call(read)
[10] tool_call(apply_patch)
[11] tool_call(apply_patch)
[12] tool_call(bash)
[13] tool_call(todowrite)
[14] tool_call(bash)
[14] thinking: I’m checking repository documentation for any mention of the old split-commit checkpoint reuse, because strategy behavior docs need to stay accurate.
[15] tool_call(read)
[16] tool_call(apply_patch)
[17] tool_call(apply_patch)
[18] tool_call(read)
[19] tool_call(apply_patch)
[20] tool_call(bash)
[21] tool_call(todowrite)
[22] tool_call(bash)
[22] thinking: The implementation and tests are updated. I’m formatting the touched Go files and then running targeted tests for the strategy package plus the changed integration test file.
[23] tool_call(bash)
[23] thinking: `gofmt` is not on PATH directly in this environment, so I’m using the repo’s `mise` task runner instead.
[24] tool_call(bash)
[24] tool_call(bash)
[24] tool_call(bash)
[24] thinking: `mise` is also unavailable in this container, so formatting/tests may be limited unless Go tooling is installed elsewhere. I’m checking the available toolchain before deciding what can be verified here.
[25] tool_call(bash)
[25] tool_call(bash)
[25] tool_call(bash)
[25] thinking: Go tooling is not installed here, and Git requires an inline `safe.directory` override because of repository ownership. I’ll still run whitespace checks and inspect the diff with that non-persistent override.
[26] thinking: There’s one helper left over from the old reuse path that is now dead code, so I’m removing it to avoid future confusion.
[26] tool_call(apply_patch)
[27] tool_call(bash)
[28] tool_call(bash)
[28] tool_call(bash)
[29] tool_call(read)
[29] tool_call(read)
[29] tool_call(read)
[29] thinking: Whitespace checks pass, but Go tests cannot run because neither `go` nor `mise` is installed in this environment. I’m doing a final diff review for correctness.
[30] tool_call(apply_patch)
[31] tool_call(apply_patch)
[32] tool_call(bash)
[33] tool_call(bash)
[33] tool_call(bash)
[33] thinking: The changed behavior is limited to normal follow-up commits after condensation. Amend restoration and deferred active-turn condensation still keep their existing ID preservation paths so already-linked commits do not lose metadata.
[34] tool_call(todowrite)

## Agent output
[35] agent: Implemented the change so normal manual follow-up commits no longer reuse the previous checkpoint ID.

**Changed**
- `cmd/entire/cli/strategy/manual_commit_hooks.go`
  - Removed the `LastCheckpointID` reuse path from `PrepareCommitMsg`.
  - If there is no new session content, the hook now skips adding an `Entire-Checkpoint` trailer.
  - Kept `PendingCheckpointID` behavior for deferred active-turn condensation.
  - Kept `LastCheckpointID` only for amend trailer restoration.
  - Removed the now-dead `getCondensedFilesTouched` helper.

- `cmd/entire/cli/integration_test/last_checkpoint_id_test.go`
  - Updated integration expectations: follow-up commits without new session content should have no checkpoint trailer.
  - Renamed/adjusted tests that previously expected split commits to share the same checkpoint ID.

- `cmd/entire/cli/session/state.go`
- `cmd/entire/cli/strategy/manual_commit_session.go`
- `cmd/entire/cli/strategy/manual_commit_test.go`
  - Updated comments/tests to reflect that `LastCheckpointID` is for amend restoration, not follow-up commit reuse.

**Verification**
- `git -c safe.directory=/entire-cli diff --check` passed.
- Could not run `gofmt`, unit tests, or integration tests because this environment does not have `go`, `gofmt`, or `mise` installed.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
diff --git a/cmd/entire/cli/integration_test/last_checkpoint_id_test.go b/cmd/entire/cli/integration_test/last_checkpoint_id_test.go
index f30e742..1576f48 100644
--- a/cmd/entire/cli/integration_test/last_checkpoint_id_test.go
+++ b/cmd/entire/cli/integration_test/last_checkpoint_id_test.go
@@ -11,16 +11,16 @@ import (
 	"github.com/entireio/cli/cmd/entire/cli/strategy"
 )
 
-// TestShadowStrategy_LastCheckpointID_ReusedAcrossCommits tests that when a user
-// commits Claude's work across multiple commits without entering new prompts,
-// all commits reference the same checkpoint ID.
+// TestShadowStrategy_LastCheckpointID_NotReusedAcrossCommits tests that when a user
+// commits again without entering a new prompt, the follow-up commit does not reuse
+// the previous checkpoint ID.
 //
 // Flow:
 // 1. Claude session edits files A and B
 // 2. User commits file A (with hooks) → condensation, LastCheckpointID saved
-// 3. User commits file B (with …

## Turn 3
**Timing:** Elapsed: 5min 23s, this turn took 16s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Yes, it’s worth testing. This is a user-visible invariant now:

`normal follow-up manual commits without new session content must not get an Entire-Checkpoint trailer`.

That is not “testing something that shouldn’t be there”; it’s testing the absence of the old bug/behavior.

I’d keep this at two levels:

- Integration test: valuable because the bug only really appears across `prepare-commit-msg` + commit + `post-commit` + session state. I already updated the existing integration tests to make that intent explicit.
- Focused unit/regression test: optional but useful if we can set it up cleanly. It would call `PrepareCommitMsg` with a session that has `LastCheckpointID` but no new content, then assert the commit message file remains unchanged.

The important distinction:

- `LastCheckpointID` should still be tested for amend restoration.
- `PendingCheckpointID` should still be tested for deferred active-turn condensation.
- Normal follow-up commits should be tested to prove they do not reuse either accidentally.

So yes: this is exactly the kind of behavior worth locking down because otherwise the old “same checkpoint ID on two commits” behavior can easily come back during future refactors.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 4min 15s, this turn took 4min 15s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 5min 58s, this turn took 37s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(bash)
[1] thinking: Let me run the formatting and lint checks to make sure the change is clean:
[2] tool_call(bash)
[3] thinking: No `go vet` errors. Let me now run the tests:
[3] tool_call(bash)

## Agent output
[4] agent: All tests pass. The single-line change is correct:

- **Before**: `len(filesToCheck) == 0 || hasOverlappingFiles(...)` — empty file list = unconditional reuse
- **After**: `len(filesToCheck) > 0 && hasOverlappingFiles(...)` — only reuse when file data is available AND files overlap

This prevents unrelated sequential commits from incorrectly inheriting the same checkpoint ID.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 6min 49s, this turn took 6min 49s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 6min 3s, this turn took 8s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: You're right, I apologize. Let me step back and give you a clear summary.

## Bug Found: Duplicate Checkpoint IDs

**Root cause:** In `PrepareCommitMsg` (`manual_commit_hooks.go:393-399`), when a new checkpoint ID is generated, it's written to the commit message trailer but **never persisted to the session state file**. The `state.PendingCheckpointID` field is never set on disk.

**How it happens:**

1. `PrepareCommitMsg` runs → generates `"abc123def456"` → trailer written to `.git/COMMIT_EDITMSG`
2. User completes the commit → `PostCommit` fires → condensation runs but **fails** (e.g., git push error)
3. `condenseAndUpdateState` returns early on error → session state is **not saved** → `PendingCheckpointID` remains `""`
4. User makes another commit → `PrepareCommitMsg` runs again → `PendingCheckpointID=""` → generates **a new ID** `"xyz789abc123"`
5. **Result:** Two commits with different `Entire-Checkpoint` trailers, each linking to different metadata paths

**The fix:** After generating a new checkpoint ID in `PrepareCommitMsg`, immediately persist it to all sessions by setting `state.PendingCheckpointID` and calling `s.saveSessionState(state)`. This ensures the same ID is reused if the commit is retried or condensation fails.

**Also affected:** The `addTrailerForAgentCommit` path (line 1080-1086) has the same bug — generates an ID but never persists it.

Do you want me to proceed with implementing the fix?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 3
**Timing:** Elapsed: 6min 19s, this turn took 13s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(invalid)

## Agent output
[2] agent: <invoke name="invalid">
<parameter name="tool">bash</parameter>
<parameter name="error">Invalid input for tool bash: JSON parsing failed: Text: {"command": "printf '%s\\n' 'with open(\"/entire-cli/cmd/entire/cli/strategy/manual_commit_hooks.go\", \"r\") as f:' ' content = f.read()' 'old = \"\\t\\tcheckpointID = cpID\\\\n\\t\\t}\\\\n\\t}\\\\n\\t// Otherwise checkpointID is already set to LastCheckpointID from above\"' 'new = \"\\t\\tcheckpointID = cpID\\\\n\\t\\t\\t// Persist the new ID to all sessions with new content so it is reused\\\\n\\t\\t\\t// if the commit is retried (user abandons the editor) or if condensation\\\\n\\t\\t\\t// fails in PostCommit. Without this, each retry would generate a new ID,\\\\n\\t\\t\\t// causing duplicate IDs across commits.\\\\n\\t\\t\\tfor _, state := range sessionsWithContent {\\\\n\\t\\t\\t\\tstate.PendingCheckpointID = checkpointID.String()\\\\n\\t\\t\\t\\tif err := s.saveSessionState(state); err != nil {\\\\n\\t\\t\\t\\t\\tlogging.Warn(logCtx, \\\"prepare-commit-msg: failed to persist checkpoint ID\\\",\\\\n\\t\\t\\t\\t\\t\\tslog.String(\\\"session_id\\\", state.SessionID),\\\\n\\t\\t\\t\\t\\t\\tslog.String(\\\"error\\\", err.Error()),\\\\n\\t\\t\\t\\t\\t)\\\\n\\t\\t\\t\\t}\\\\n\\t\\t\\t}\\\\n\\t\\t}\\\\n\\t}\\\\n\\t// Otherwise checkpointID is already set to LastCheckpointID from above\"' 'if old not in content:' '    print(\"ERROR: old string not found\")' 'else:' '    content = content.replace(old, new, 1)' '    with open(\"/entire-cli/cmd/entire/cli/strategy/manual_commit_hooks.go\", \"w\") as f:' '        f.write(content)' '    print(\"SUCCESS\")' > /tmp/fix_hooks.py && python3 /tmp/fix_hooks.py", "description": "Write and run fix script".
Error message: JSON Parse error: Expected '}'</parameter>
</invoke>
</minimax:tool_call>

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 8min 3s, this turn took 2min 40s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(bash)
[2] tool_call(bash)
[3] tool_call(bash)
[4] thinking: The first fix is in. Now let me also fix `addTrailerForAgentCommit` which has the same issue:
[4] tool_call(bash)
[5] tool_call(bash)
[6] tool_call(bash)
[7] tool_call(bash)
[8] thinking: Both fixes applied. Now let me run the tests:
[8] tool_call(bash)
[9] tool_call(bash)
[10] tool_call(bash)
[11] tool_call(bash)
[12] tool_call(bash)
[13] thinking: All tests pass. Let me also run linting and formatting:
[13] tool_call(bash)
[14] tool_call(bash)
[15] tool_call(bash)
[16] tool_call(bash)
[17] tool_call(bash)
[18] tool_call(todowrite)

## Agent output
[19] agent: Done. Here's a summary of the fix:

## Changes Made

**File:** `cmd/entire/cli/strategy/manual_commit_hooks.go`

**Two locations fixed:**

1. **`PrepareCommitMsg` (line ~398):** After generating a new checkpoint ID, the code now persists it to all sessions with new content by setting `state.PendingCheckpointID` and calling `s.saveSessionState(state)`. This ensures the same ID is reused if the commit is retried or condensation fails.

2. **`addTrailerForAgentCommit` (line ~1098):** Same fix for the agent-commit fast path — persists the generated ID to the session state before the trailer is written.

**Tests:** All pass (`go test ./cmd/entire/cli/strategy/...`)  
**Build:** Compiles cleanly (`go build -buildvcs=false ./...`)  
**Vet:** No issues (`go vet ./cmd/entire/cli/strategy/...`)

The core invariant is now guaranteed: a checkpoint ID is written to disk as `PendingCheckpointID` before it appears in any commit message, so retries always reuse the same ID.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
diff --git a/cmd/entire/cli/strategy/manual_commit_hooks.go b/cmd/entire/cli/strategy/manual_commit_hooks.go
index b5f9279..369b9e5 100644
--- a/cmd/entire/cli/strategy/manual_commit_hooks.go
+++ b/cmd/entire/cli/strategy/manual_commit_hooks.go
@@ -396,6 +396,19 @@ func (s *ManualCommitStrategy) PrepareCommitMsg(commitMsgFile string, source str
 				return fmt.Errorf("failed to generate checkpoint ID: %w", err)
 			}
 			checkpointID = cpID
+			// Persist the new ID to all sessions with new content so it is reused
+			// if the commit is retried (user abandons the editor) or if condensation
+			// fails in PostCommit. Without this, each retry would generate a new ID,
+			// causing duplicate IDs across commits.
+			for _, state := range sessionsWithContent {
+				state.PendingCheckpointID = checkpointID.String()
+				if err := s.saveSessionState(state); err != nil {
+					logging.Warn(logCtx, "prepare-commit-msg: failed to persist checkpoint ID",
+						slog.String("session_id", state.SessionID),
+						slog.String("error", err.Error()),
+					)
+				}
+			}
 		}
 	}
 	// Otherwise checkpointID is already set to LastCheckpointID from above
@@ -1083,6 +1096,15 @@ func (s *ManualCommitStrategy) addTrailerForAgentCommit(logCtx context.Context,
 		if err != nil {
 			return nil //nolint:nilerr // Hook must be silent on failure
 		}
+		// Persist the new ID so it is reused if the commit is retried or
+		// if condensation fails in PostCommit.
+		state.PendingCheckpointID = cpID.String()
+		if err := s.saveSessionState(state); err != nil {
+			logging.Warn(logCtx, "prepare-commit-msg: agent commit failed to persist checkpoint ID",
+				slog.String("session_id", state.SessionID),
+				slog.String("error", err.Error()),
+			)
+		}
 	}
 
 	content, err := os.ReadFile(commitMsgFile) //nolint:gosec // commitMsgFile is provided by git hook
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 5
**Timing:** Elapsed: 8min 15s, this turn took 9s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Yes, I think it's worth adding tests here. This was a real bug, and the tests would serve as regression tests to document the expected behavior and prevent it from reoccurring.

The specific scenarios to test:

1. **Generate then retry** — call `PrepareCommitMsg` once (generates an ID), then call it again (should reuse the same ID, not generate a new one)
2. **Persistence across failure** — verify that after generating an ID, the session state file actually contains `PendingCheckpointID`

These would live in `phase_prepare_commit_msg_test.go` alongside the existing amend tests, and would use the same patterns already there. Want me to add them?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-3) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 1
**Timing:** Elapsed: 2min 27s, this turn took 2min 27s
** The agent is signaling completion.

## Task
when using the cli I just noticed an issue that two manual commits after each other had the same checkpoint id, can you check how this can happen, this shouldn't be a thing, right?


## Repository Configuration Files

The following configuration files were found in the repository. Follow any project-specific guidelines they contain.

### CLAUDE.md

# Entire - CLI 

This repo contains the CLI for Entire.

## Architecture

- CLI build with github.com/spf13/cobra and github.com/charmbracelet/huh 

## Key Directories

### Commands (`cmd/`)
- `entire/`: Main CLI entry point
- `entire/cli`: CLI utilities and helpers
- `entire/cli/commands`: actual command implementations
- `entire/cli/strategy`: strategy implementations - see section below
- `entire/cli/checkpoint`: checkpoint storage abstractions (temporary and committed)
- `entire/cli/session`: session state management
- `entire/cli/integration_test`: integration tests

## Tech Stack

- Language: Go 1.25.x
- Build tool: mise, go modules
- Linting: golangci-lint

## Development

### Running Tests
```bash
mise run test
```

### Running Integration Tests
```bash
mise run test:integration
```

### Running All Tests (CI)
```bash
mise run test:ci
```

Integration tests use the `//go:build integration` build tag and are located in `cmd/entire/cli/integration_test/`.

### Test Parallelization

**Always use `t.Parallel()` in tests.** Every top-level test function and subtest should call `t.Parallel()` unless it modifies process-global state (e.g., `os.Chdir()`).

```go
func TestFeature_Foo(t *testing.T) {
    t.Parallel()
    // ...
}

// Integration tests: RunForAllStrategies handles t.Parallel() for subtests internally,
// but the top-level test still needs it
func TestFeature_Bar(t *testing.T) {
    t.Parallel()
    RunForAllStrategies(t, func(t *testing.T, env *TestEnv, strategyName string) {
        // ...
    })
}
```

**Exception:** Tests that modify process-global state cannot be parallelized. This includes `os.Chdir()`/`t.Chdir()` and `os.Setenv()`/`t.Setenv()` — Go's test framework will panic if these are used after `t.Parallel()`.

### Linting and Formatting
```bash
mise run fmt && mise run lint
```

### Before Every Commit (REQUIRED)

**CI will fail if you skip these steps:**

```bash
mise run fmt      # Format code (CI enforces gofmt)
mise run lint     # Lint check (CI enforces golangci-lint)
mise run test:ci  # Run all tests (unit + integration)
```

Or combined: `mise run fmt && mise run lint && mise run test:ci`

**Common CI failures from skipping this:**
- `gofmt` formatting differences → run `mise run fmt`
- Lint errors → run `mise run lint` and fix issues
- Test failures → run `mise run test` and fix

### Code Duplication Prevention

Before implementing Go code, use `/go:discover-related` to find existing utilities and patterns that might be reusable.

**Check for duplication:**
```bash
mise run dup           # Comprehensive check (threshold 50) with summary
mise run dup:staged    # Check only staged files
mise run lint          # Normal lint includes dupl at threshold 75 (new issues only)
mise run lint:full     # All issues at threshold 75
```

**Tiered thresholds:**
- **75 tokens** (lint/CI) - Blocks on serious duplication (~20+ lines)
- **50 tokens** (dup) - Advisory, catches smaller patterns (~10+ lines)

When duplication is found:
1. Check if a helper already exists in `common.go` or nearby utility files
2. If not, consider extracting the duplicated logic to a shared helper
3. If duplication is intentional (e.g., test setup), add a `//nolint:dupl` comment with explanation

## Code Patterns

### Error Handling

The CLI uses a specific pattern for error output to avoid duplication between Cobra and main.go.

**How it works:**
- `root.go` sets `SilenceErrors: true` globally - Cobra never prints errors
- `main.go` prints errors to stderr, unless the error is a `SilentError`
- Commands return `NewSilentError(err)` when they've already printed a custom message

**When to use `SilentError`:**
Use `NewSilentError()` when you want to print a custom, user-friendly error message instead of the raw error:

```go
// In a command's RunE function:
if _, err := paths.RepoRoot(); err != nil {
    cmd.SilenceUsage = true  // Don't show usage for prerequisite errors
    fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
    return NewSilentError(errors.New("not a git repository"))
}
```

**When NOT to use `SilentError`:**
For normal errors where the default error message is sufficient, just return the error directly. main.go will print it:

```go
// Normal error - main.go will print "unknown strategy: foo"
return fmt.Errorf("unknown strategy: %s", name)
```

**Key files:**
- `errors.go` - Defines `SilentError` type and `NewSilentError()` constructor
- `root.go` - Sets `SilenceErrors: true` on root command
- `main.go` - Checks for `SilentError` before printing

### Settings

All settings access should go through the `settings` package (`cmd/entire/cli/settings/`).

**Why a separate package:**
The `settings` package exists to avoid import cycles. The `cli` package imports `strategy`, so `strategy` cannot import `cli`. The `settings` package provides shared settings loading that both can use.

**Usage:**
```go
import "github.com/entireio/cli/cmd/entire/cli/settings"

// Load full settings object
s, err := settings.Load()
if err != nil {
    // handle error
}
if s.Enabled {
    // ...
}

// Or use convenience functions
if settings.IsSummarizeEnabled() {
    // ...
}
```

**Do NOT:**
- Read `.entire/settings.json` or `.entire/settings.local.json` directly with `os.ReadFile`
- Duplicate settings parsing logic in other packages
- Create new settings helpers without adding them to the `settings` package

**Key files:**
- `settings/settings.go` - `EntireSettings` struct, `Load()`, …

## Turn 2
**Timing:** Elapsed: 12min 1s, this turn took 9min 29s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(read)
[2] tool_call(read)
[3] tool_call(read)
[4] tool_call(bash)
[5] tool_call(bash)
[6] tool_call(read)
[7] tool_call(bash)
[8] tool_call(bash)
[9] tool_call(read)
[10] tool_call(read)
[11] tool_call(read)
[12] tool_call(bash)
[13] tool_call(read)
[14] thinking: Now I have a clear picture. Let me implement the fix.
[14] tool_call(edit)
[15] thinking: Now let me write a test that surfaces the bug. Let me check existing test patterns for staging files and verify how `findSessionsForWorktree` filters.
[15] tool_call(read)
[16] tool_call(bash)
[17] tool_call(read)
[18] tool_call(bash)
[19] tool_call(bash)
[20] tool_call(read)
[21] tool_call(read)
[22] tool_call(read)
[23] tool_call(read)
[24] tool_call(bash)
[25] tool_call(bash)
[26] thinking: Now let me append the tests:
[26] tool_call(edit)
[27] tool_call(edit)
[28] thinking: Now let me verify the fix and tests compile and pass. First let me check `time` is still used in the file (I kept the import).
[28] tool_call(bash)
[29] tool_call(bash)
[30] tool_call(bash)
[31] tool_call(bash)
[32] tool_call(bash)
[33] tool_call(bash)
[34] thinking: Clean build and vet. Now run the new tests:
[34] tool_call(bash)
[35] thinking: All three pass. Let me verify the bug test actually fails on the original code by temporarily reverting the fix:
[35] tool_call(bash)
[36] tool_call(bash)
[37] tool_call(bash)
[38] thinking: The bug test fails on original code (trailer added with `abc123def456` — the duplicate ID). With the fix applied it passes. Now let me run the full strategy test suite to ensure no regressions:
[38] tool_call(bash)
[39] tool_call(bash)
[40] thinking: All existing reuse/amend tests still pass. Now run fmt and lint:
[40] tool_call(bash)
[41] tool_call(bash)
[42] tool_call(bash)
[43] tool_call(bash)
[44] tool_call(bash)
[45] tool_call(bash)
[46] thinking: Zero new issues. Let me run the broader test suite to make sure nothing else broke:
[46] tool_call(bash)
[47] thinking: All tests pass. Let me also run the integration tests since they exercise the full prepare-commit-msg → post-commit flow:
[47] tool_call(bash)

## Agent output
[48] agent: All integration tests pass too. Let me summarize the work.

## Summary

You were right — two consecutive manual commits sharing the same checkpoint ID **shouldn't** happen for unrelated commits. It was a real bug.

### Root cause

In `PrepareCommitMsg` (`cmd/entire/cli/strategy/manual_commit_hooks.go`), the "no new content" branch tries to reuse `session.LastCheckpointID` for split-commit linking. When the session had already been condensed (`FilesTouched` nil, `StepCount == 0`), it fell back to reading condensed `files_touched` from `entire/checkpoints/v1`. But the guard was:

```go
if len(filesToCheck) == 0 || hasOverlappingFiles(stagedFiles, filesToCheck) {
    checkpointID = session.LastCheckpointID  // reuse
```

The `len(filesToCheck) == 0 ||` clause meant that whenever `getCondensedFilesTouched` returned nothing (checkpoint branch missing, summary unreadable, or `files_touched` empty), the checkpoint ID was **reused unconditionally** — even for a commit whose staged files had zero overlap with the session's work. That's how two unrelated commits ended up with the same `Entire-Checkpoint` trailer.

### Fix

`cmd/entire/cli/strategy/manual_commit_hooks.go:331-365` — restructured the reuse decision into two explicit cases:
- **Post-condensation** (`FilesTouched` empty AND `StepCount == 0`): reuse **only if** condensed `files_touched` can be retrieved AND overlaps staged files. If condensed metadata is unavailable, skip the trailer instead of linking an unrelated commit.
- **Mid-flight** (everything else): preserves the original behavior (reuse when `FilesTouched` overlaps, or when `FilesTouched` is empty but the session is active).

### Tests

Added 3 tests in `cmd/entire/cli/strategy/phase_prepare_commit_msg_test.go`:
- `TestPrepareCommitMsg_PostCondensation_NoCondensedMetadata_NoTrailer` — reproduces the bug (fails on original code, passes with fix).
- `TestPrepareCommitMsg_PostCondensation_OverlappingCondensedFiles_ReusesTrailer` — guards the legitimate split-commit reuse path so the fix doesn't over-correct.
- `TestPrepareCommitMsg_PostCondensation_NonOverlappingCondensedFiles_NoTrailer` — sibling case: condensed metadata present but no overlap → no trailer.

### Verification

- `go build`, `go vet`, `gofmt`: clean
- `golangci-lint --new`: 0 new issues
- Full unit test suite: passing
- Integration tests (`-tags=integration`): passing

I did not commit anything, per the repo guidelines. Let me know if you'd like me to commit the fix.

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-0) ===
diff --git a/cmd/entire/cli/strategy/common.go b/cmd/entire/cli/strategy/common.go
index 211c420..a69c3d8 100644
--- a/cmd/entire/cli/strategy/common.go
+++ b/cmd/entire/cli/strategy/common.go
@@ -772,13 +772,13 @@ func checkCanRewind() (bool, string, error) {
 	var msg strings.Builder
 	msg.WriteString("You have uncommitted changes:\n")
 	for _, f := range modified {
-		msg.WriteString(fmt.Sprintf("  modified:   %s\n", f))
+		fmt.Fprintf(&msg, "  modified:   %s\n", f)
 	}
 	for _, f := range added {
-		msg.WriteString(fmt.Sprintf("  added:      %s\n", f))
+		fmt.Fprintf(&msg, "  added:      %s\n", f)
 	}
 	for _, f := range deleted {
-		msg.WriteString(fmt.Sprintf("  deleted:    %s\n", f))
+		fmt.Fprintf(&msg, "  deleted:    %s\n", f)
 	}
 	msg.WriteString("\nPlease commit or stash your changes before rewinding.")
 
@@ -919,15 +919,15 @@ func checkCanRewindWithWarning() (bool, string, error) {
 			stats = fmt.Sprintf("-%d", c.removed)
 		}
 
-		msg.WriteString(fmt.Sprintf("  %-10s %s", c.status+":", c.filename))
+		fmt.Fprintf(&msg, "  %-10s %s", c.status+":", c.filename)
 		if stats != "" {
-			msg.WriteString(fmt.Sprintf(" (%s)", …

## Turn 3
**Timing:** Elapsed: 13min 37s, this turn took 25s
** The agent is signaling completion.

## Agent activity (this turn)
(no intermediate steps)

## Agent output
[1] agent: Honest answer: **test 1 is clearly worth it; tests 2 and 3 are debatable.**

**Test 1** (`NoCondensedMetadata_NoTrailer`) reproduces the exact bug you reported. That's the textbook "write a test that surfaces the bug first" case — it documents the user-facing contract ("unrelated commits don't get a checkpoint ID") and guards the regression. Keep it unconditionally.

**Test 2** (`OverlappingCondensedFiles_ReusesTrailer`) is a regression guard for the split-commit reuse path that the fix could have broken. Worth keeping *if* you consider split-commit linking a feature you want to preserve. It's not testing the bug; it's testing "don't over-correct." Reasonable but not essential.

**Test 3** (`NonOverlappingCondensedFiles_NoTrailer`) is the one I'd question. It tests the same *intent* as test 1 ("unrelated commit → no trailer") just via a different branch (`hasOverlappingFiles` false vs `len(condensedFiles) == 0`). It's testing branch coverage of my fix's implementation, not a distinct user-facing behavior. If you believe tests should document intent rather than cover branches, test 3 is the one that's "testing something that shouldn't be there" — it's locking in the file-overlap heuristic, which is itself a somewhat fragile workaround.

My recommendation: **keep 1 and 2, drop 3.** If you'd rather be maximalist on regression coverage, keep all three. Want me to remove test 3?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-1) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.

## Turn 4
**Timing:** Elapsed: 15min 49s, this turn took 2min 5s
** The agent is signaling completion.

## Agent activity (this turn)
[1] tool_call(bash)
[2] tool_call(bash)
[3] tool_call(read)
[4] tool_call(bash)
[5] tool_call(read)
[6] tool_call(read)
[7] tool_call(read)
[8] thinking: Let me verify exactly which of my tests reproduce the bug vs. just test the new behavior:
[8] tool_call(bash)
[9] tool_call(bash)
[10] tool_call(bash)
[11] tool_call(bash)
[12] thinking: The fix was already committed by a background process. Let me revert just the hooks file to verify which tests reproduce the bug:
[12] tool_call(bash)
[13] tool_call(bash)
[14] thinking: Now restore the fix and review the existing test landscape:
[14] tool_call(bash)

## Agent output
[15] agent: Here's what the existing test landscape shows:

## Existing coverage

**Integration tests** (`integration_test/`):
- `TestShadowStrategy_LastCheckpointID_ReusedAcrossCommits` (last_checkpoint_id_test.go:23) — the **positive** split-commit case: fileA + fileB both from Claude, both condensed → both commits share the checkpoint ID. ✅
- `TestShadowStrategy_MidSessionCommit_NoTrailerForUnrelatedFile` (mid_session_commit_test.go:139) — unrelated staged file → no trailer. **But this tests the mid-session live-transcript path (`sessionHasNewContentFromLiveTranscript`), NOT the post-condensation `getCondensedFilesTouched` path where the bug was.**
- `TestShadowStrategy_LastCheckpointID_IgnoresOldSessions`, `NotSetWithoutCondensation` — adjacent but not the bug.

**Unit tests** (`strategy/`):
- `TestShadowStrategy_PrepareCommitMsg_ReusesLastCheckpointID` (manual_commit_test.go:1380) — not a behavioral test, just verifies state save/load. Its own comment admits "We can't fully test PrepareCommitMsg... The actual behavior is tested through integration tests."

## The gap

**No existing test covers the actual bug scenario**: a *post-condensation* session (condensed, `LastCheckpointID` set, `FilesTouched` nil) where a second commit stages a file *unrelated* to the condensed `files_touched`. That's exactly what you reported, and it slipped through because the closest test (`MidSessionCommit_NoTrailerForUnrelatedFile`) exercises the wrong code path.

## My 3 unit tests — verified against original code

I just ran them against the unpatched code:

| Test | On original code | Verdict |
|------|------------------|---------|
| `NoCondensedMetadata_NoTrailer` | **FAILS** (reproduces bug) | **Keep** — essential |
| `OverlappingCondensedFiles_ReusesTrailer` | passes | Borderline redundant with `LastCheckpointID_ReusedAcrossCommits` integration test |
| `NonOverlappingCondensedFiles_NoTrailer` | passes | **Drop** — tests pre-existing correct behavior (the `hasOverlappingFiles==false` branch already worked); locks in implementation detail, doesn't reproduce the bug |

## Recommendation

1. **Keep test 1** — it's the bug reproducer.
2. **Drop test 3** — doesn't reproduce the bug, tests a branch that already worked.
3. **Replace test 2 with an integration test** that mirrors `TestShadowStrategy_LastCheckpointID_ReusedAcrossCommits` but commits an *unrelated* file second. That's the true end-to-end regression guard for your scenario, and it fills the actual gap in the integration suite (which has the positive reuse case but not the negative post-condensation case).

Want me to drop test 3 and add the integration test?

## Code changes (this turn)
```diff
=== /entire-cli (incremental vs harbor-turn-2) ===
```

Pick ONE tool. Default to no-op unless you have a clear, new reason to speak.