fix(agent-sync): reconcile native publication outcomes

[namastex888]

Context

Post-merge closure for review findings discovered while #2588 was still being audited. This branch is rebased onto current dev, including #2588 and the adjacent #2589 lock-quarantine repair.

Fixes

• Centralize Darwin renamex_np and Linux renameat2 regular-file publication behind one exact-outcome reconciler.
  • Native capability setup unavailable: use the verified portable hard-link transaction.
  • Native nonzero result: preserve the no-clobber failure.
  • Exception before the syscall commits: fail closed with no portable retry.
  • Exception after the syscall commits: recognize the commit only when the staged name is absent and the target has the exact staged inode identity and bytes with a stable re-stat.
  • Injected Linux capability probes do not reuse the process-global memoized probe.
• Let missing-home publication select its dedicated portable mkdir commit when Darwin FFI setup is unavailable.
• Remove both post-release pathname-only empty-home deletions from full uninstall. Identity-bound lock cleanup remains authoritative, so a foreign GENIE_HOME replacement is never deleted.
• Add deterministic Darwin/Linux pre- and post-syscall regressions plus the full-uninstall foreign-home swap regression.

Validation

• bun test src/lib/agent-sync.test.ts -t 'claude agent fan-out|cross-process sync lock' — 64 pass
• bun test src/genie-commands/uninstall.test.ts — 74 pass
• bun run check:fast — pass
• git diff --check origin/dev...HEAD — pass
• Independent final review — SHIP, no CRITICAL/HIGH gaps

Scope note

The pre-existing shared publishDirectoryViaNameClaim claim-to-rename advisory remains outside this regular-file and dedicated lock-home repair. Neither portable path changed here reaches that primitive.

Summary by CodeRabbit

• Bug Fixes

  • Improved uninstall behavior when the installation directory changes during removal, preserving lock files and existing state backups.
  • Prevented sync updates from overwriting existing agent manifests or installation directories.
  • Improved recovery after interrupted or partially completed publication operations.
  • Added safer platform-specific handling, including portable fallbacks when native operations are unavailable and clear failures when they cannot be completed safely.

• Tests

  • Expanded coverage for uninstall and cross-platform synchronization scenarios.

[coderabbitai]

📝 Walkthrough

Walkthrough

The change makes native no-clobber publication injectable and failure-aware across manifests and GENIE_HOME creation. Uninstall cleanup now uses lock-preserving install-state removal instead of empty-directory deletion, with tests covering native failures and swapped-in GENIE_HOME directories.

Changes

Agent sync publication and uninstall

Layer / File(s)	Summary
Native capability contracts and resolution src/lib/agent-sync.ts	Publication options now accept injected no-clobber dependencies, with platform-specific Linux and Darwin capability resolution.
Manifest no-clobber publication src/lib/agent-sync.ts, src/lib/agent-sync.test.ts	Manifest publishing wires injected dependencies into atomic publication, validates staged content, reconciles native exceptions, and tests fallback and fail-closed outcomes.
GENIE_HOME publication behavior src/lib/agent-sync.ts, src/lib/agent-sync.test.ts	GENIE_HOME creation selects native or portable publication and tests Darwin fallback and native failure behavior.
Lock-aware GENIE_HOME cleanup src/genie-commands/uninstall.ts, src/genie-commands/uninstall.test.ts	Uninstall removes eligible state through the preserving cleanup path, eliminates empty-directory removal, and tests a swapped-in GENIE_HOME while the sync lock is held.

Estimated code review effort: 4 (Complex) | ~45 minutes

Possibly related PRs

• automagik-dev/genie#2583: Also changes lock-aware genie uninstall handling for GENIE_HOME and agent-sync state.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes the main change: reconciling native publication outcomes in agent-sync.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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• Create PR with unit tests
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[namastex888]

@coderabbitai review

[coderabbitai]

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[gemini-code-assist]

Code Review

This pull request introduces native Darwin support for atomic, no-clobber file and directory publishing using renamex_np via dlopen, alongside comprehensive test coverage and dependency injection seams for testing native platform fallbacks. It also removes the automatic cleanup of empty GENIE_HOME directories during uninstallation. The feedback highlights a critical issue where closing the libc handle inside the returned Darwin rename function makes it single-use, which could lead to failures if the function is invoked multiple times.

Important

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[coderabbitai]

Actionable comments posted: 3

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/lib/agent-sync.ts`:
- Around line 6246-6270: Extract the shared staged-to-target publishing closure
from the Darwin and Linux branches into a helper such as
makeAgentSyncHomePublisher, accepting the resolved rename function and
preserving the existing lstatSafe detail selection and NoClobberPublishError
message. Have both branches return this helper after resolving their
platform-specific renamer, leaving platform detection and null handling
unchanged.
- Around line 6240-6271: Update resolveNativeAgentSyncHomePublisher to use the
shared platform value from options.homePublishDeps.platform instead of reading
process.platform directly, while preserving the existing Darwin and Linux branch
behavior and fallback handling.
- Around line 2134-2184: Cache the result of the Darwin opener capability probe
used by resolveDarwinRenameExclusive, so defaultDarwinRenameOpener does not
perform dlopen/dlclose for every publish call. Memoize it once per process or
sync run while preserving dependency-injected darwinOpener behavior and the
existing portable fallback when FFI setup is unavailable.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

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Run ID: c05dc20b-08c9-447b-993a-a0f837c62f92

📥 Commits

Reviewing files that changed from the base of the PR and between e594af9 and 0ef3727.

📒 Files selected for processing (4)

• src/genie-commands/uninstall.test.ts
• src/genie-commands/uninstall.ts
• src/lib/agent-sync.test.ts
• src/lib/agent-sync.ts

💤 Files with no reviewable changes (1)

• src/genie-commands/uninstall.ts