[kartsan03]

Description

Two more paths re-register installed extensions and presets after the integration manifest is written, but never refresh the hashes of files those presets rewrite: specify init --force into an existing project, and the rollback after a failed specify integration switch. A preset that overrides a core command then leaves a stale hash, integration status reports the file as modified, and integration upgrade refuses without --force. This is the gap Copilot named on #5145 ("init --force, and switch rollback still skip them"); #5145 fixed switch and use.

init --force saves a fresh manifest right before registration, the same situation as upgrade (#4696) and a switch to a new target. It now calls _resync_manifest_after_registration with every tracked file, so files registration didn't change keep their recovered markers. After init --force the project is in sync, including one where an earlier preset command had left a stale hash.

The rollback restores an integration whose manifest was written when it was installed, like use. It now takes _snapshot_manifest_before_registration() before re-registering and refreshes only files that were unmodified before and changed by registration. A file the user edited earlier keeps its old hash and is still reported as modified. Both steps are best-effort: a missing or corrupt manifest, or a failed save, prints a warning, and the switch error stays the primary message with exit code 1.

The uninstall fallback (integration uninstall of the default integration) has the same gap. I left it out because #5100 rewrites command_uninstall.py and moves that code into _operation_uninstall.py.

Repro with the real CLI and the preset from #5078 (overrides speckit.tasks). For the rollback, a plain file named .gemini makes the Gemini install fail:

# init --force
specify init --here --integration codex --script sh --ignore-agent-tools --non-interactive --offline
specify preset add --dev ../tasks-preset
specify init --here --force --integration codex --script sh --ignore-agent-tools --non-interactive --offline
specify integration upgrade codex --script sh

# failed switch
specify init --here --integration claude --script sh --ignore-agent-tools --non-interactive --offline
specify integration install codex --script sh
specify preset add --dev ../tasks-preset
printf 'not a directory\n' > .gemini
specify integration switch gemini --script sh   # exit 1: Not a directory: '.../.gemini/commands'; codex becomes the default
specify integration upgrade codex --script sh

Step	main (2a23a84)	This PR
integration status after init --force	WARNING, 1 modified file	OK, 0 modified
upgrade codex after init --force	exit 1, "1 file(s) have been modified since installation"	exit 0
integration status after the failed switch	WARNING, 1 modified file	OK, 0 modified
upgrade codex after the failed switch	exit 1, same message	exit 0

Refs #5078

Testing

• Tested locally with uv run specify --help
• Ran existing tests with uv sync && uv run pytest
• Tested with a sample project (if applicable)

New tests, through the CLI with a real preset:

• test_command_init.py::test_init_force_syncs_manifest_hash_for_preset_override: after init --force the hash matches the preset-rendered skill, status shows 0 modified files and upgrade without --force exits 0. init --force still replaces a user-edited skill, as on main.
• test_command_init.py::test_init_force_keeps_recovered_markers: a recovered file that registration doesn't touch stays recovered.
• test_command_switch.py::test_failed_switch_syncs_fallback_manifest_without_blessing_user_edits[None|plan|tasks]: after the rollback the fallback's hash matches the file; a skill the user edited before the switch (plan, which the preset doesn't touch, and tasks, which it rewrites) keeps its old hash and upgrade still refuses.
• test_command_switch.py::test_failed_switch_manifest_refresh_is_best_effort[missing|corrupt|save-error]: registration still runs, a missing manifest isn't created, a corrupt one is left as it is, and the original switch error and exit code survive.

With the two source files reverted to main, 5 of the 8 cases fail. The tasks edit case, the missing-manifest case and the recovered-marker test pass on main too, since main never re-hashes. With the unmodified_files argument removed from the rollback, both edit cases fail with "pre-existing edits must not be recorded as pristine"; removed from init, the recovered-marker test fails. With the fallback_manifest is not None check removed, the missing and corrupt cases fail.

Full suite on Linux, Python 3.13: 13450 passed, 441 skipped (uv sync --extra test, then pytest -n 2, 9 min). Ruff 0.15.0 (ruff check src tests) passes. I haven't run it on Windows.

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (fill in the disclosure below)

AI disclosure: Codex CLI (model: gpt-6.1-sol, reasoning effort xhigh, autonomous, offline sandbox) reproduced the paths on main and wrote the fix and the tests. Claude Code (model: claude-opus-5-5, autonomous) reviewed the change, reran the repro with the real CLI on main and the branch, ran the full suite and lint, and drafted this description. The commit carries Assisted-by: trailers for both.

[Copilot]

🟢 Approval recommended

No active review issues remain for the manifest-hash synchronization changes.

No open issues 🎉

What changed in this PR

Closes the remaining manifest-hash gaps after preset registration in init --force and failed integration-switch rollback, extending the fixes from #5145. This prevents legitimate preset overrides from appearing as user modifications and blocking later upgrades.

Changes:

• Refreshes hashes after forced reinitialization while preserving recovered markers on unchanged files.
• Refreshes rollback hashes selectively, preserving pre-existing modification detection and the original switch error.
• Adds regression coverage for preset overrides, user edits, recovered markers, and manifest failures.

Before-and-after regression results are documented in the PR; tests were not rerun here.

File	Description
tests/​specify_cli/​test_command_init.py	Tests preset-hash synchronization and recovered-marker preservation.
tests/​specify_cli/​integrations/​test_command_switch.py	Tests rollback synchronization, user-edit detection, and manifest-failure handling.
src/​specify_cli/​integrations/​command_switch.py	Snapshots and selectively refreshes fallback manifest hashes during rollback.
src/​specify_cli/​command_init.py	Refreshes manifest hashes after reinitialization registration.

_{Review effort: Balanced (auto)}

[mnriem]

Thank you!