Repository navigation
[Bug]: integration switch leaves the manifest out of date when a preset overrides a core command #5078
Description
Bug Description
specify integration switch <target> installs the target integration and saves its manifest (src/specify_cli/integrations/command_switch.py:309-316). It then re-registers installed presets for the target (command_switch.py:380-389). A preset that overrides a core command rewrites a file the manifest already tracks, and the manifest is not re-hashed afterwards. As a result integration status reports the file as modified, and a later integration upgrade without --force refuses to run, even though the user changed nothing.
integration upgrade handles the same situation by calling _resync_manifest_after_registration (command_upgrade.py:352, added for #4696). switch does not call it.
Steps to Reproduce
From the root of a fresh clone, after uv sync, save the script below as repro.py and run it with uv run python repro.py.
import hashlib, json, os, tempfile
from pathlib import Path
from typer.testing import CliRunner
from specify_cli import app
tmp = Path(tempfile.mkdtemp())
project = tmp / "proj"
project.mkdir()
os.chdir(project)
run = lambda *args: CliRunner().invoke(app, list(args))
run("init", "--here", "--integration", "claude", "--script", "sh", "--ignore-agent-tools")
preset = tmp / "tasks-preset"
(preset / "commands").mkdir(parents=True)
(preset / "commands" / "speckit.tasks.md").write_text(
"---\ndescription: Tasks override\n---\nPreset tasks body\n")
(preset / "preset.yml").write_text("""schema_version: '1.0'
preset: {id: tasks-preset, name: Tasks Preset, version: 1.0.0, description: x}
requires: {speckit_version: '>=0.1.0'}
provides:
templates:
- {type: command, name: speckit.tasks, file: commands/speckit.tasks.md}
""")
run("preset", "add", "--dev", str(preset))
r = run("integration", "switch", "codex", "--script", "sh")
print("switch exit code:", r.exit_code)
rel = ".agents/skills/speckit-tasks/SKILL.md"
manifest = json.loads(Path(".specify/integrations/codex.manifest.json").read_text())
on_disk = hashlib.sha256(Path(rel).read_bytes()).hexdigest()
print("preset body in skill:", "Preset tasks body" in Path(rel).read_text())
print("manifest hash matches file:", manifest["files"][rel] == on_disk)
r = run("integration", "upgrade", "codex", "--script", "sh")
print("upgrade exit code:", r.exit_code)
print(r.output.strip())The script initialises a project with Claude Code, adds a local preset that overrides speckit.tasks, switches to Codex, compares the manifest hash with the file on disk, and then runs integration upgrade codex without --force.
Expected Behavior
After the switch, the manifest hash for .agents/skills/speckit-tasks/SKILL.md matches the file that preset registration wrote, and integration upgrade codex succeeds. The docstring of _resync_manifest_after_registration (src/specify_cli/integrations/_helpers.py:486-505) says files rewritten by registration must be re-hashed "so check_modified() doesn't misreport a legitimate override as tampering", and names switch among the operations it serves. The regression test test_upgrade_force_syncs_manifest_hash_for_preset_overridden_skill (tests/specify_cli/integrations/test_command_upgrade.py:1320-1385) sets the same expectation for upgrade.
Actual Behavior
switch exit code: 0
preset body in skill: True
manifest hash matches file: False
upgrade exit code: 1
⚠ 1 file(s) have been modified since installation:
.agents/skills/speckit-tasks/SKILL.md
Use --force to overwrite modified files, or resolve manually.
Specify CLI Version
1.2.4.dev0 (main at 27d14e2)
AI Agent
Codex CLI
Operating System
Linux 6.18 (Ubuntu container)
Python Version
Python 3.12.3
Error Logs
⚠ 1 file(s) have been modified since installation:
.agents/skills/speckit-tasks/SKILL.md
Use --force to overwrite modified files, or resolve manually.
Additional Context
integration use (src/specify_cli/integrations/command_use.py) also re-registers presets without a manifest resync, so it looks affected in the same way, but I have not reproduced that path. Calling _resync_manifest_after_registration after preset registration in switch (and probably use) would likely fix it.
Also reproduced on macOS (Darwin 25.6, arm64) with Python 3.14.4 and uv run python -I repro.py against 27d14e2; the output matches the above.
AI Disclosure
Found and reproduced with Claude Code (model: Claude Opus 4.8), run autonomously under human supervision. The human reporter re-ran every reproduction above before filing.
Activity
fix(integrations): compare each file inside the resync error handler
fix(integrations): keep paths outside the project out of the snapshot
fix(integrations): check manifest paths before hashing, keep recovere…
fix(integrations): warn when the manifest snapshot skips a file
test(integrations): cover use and switch with a missing or corrupt ta…
fix(integrations): refresh manifest hashes after preset registration …
github-actions commentedon Oct 29, 2026
Bug assessment — switch-manifest-stale: Invalid · severity low
Bug Assessment:
integration switchmanifest hash drift after preset overrideintegration switchleaves the manifest out of date when a preset overrides a core command #5078Report (summarized)
Issue author @hnipps reports that
integration switchsaved a target manifest before preset re-registration, so preset-overridden files (example:.agents/skills/speckit-tasks/SKILL.md) could diverge from manifest hashes. Reported result:integration status/integration upgradethen flagged the file as modified unless--forcewas used.Issue title: "[Bug]:
integration switchleaves the manifest out of date when a preset overrides a core command".No additional comments were present.
Symptom
Reported behavior: after switching integrations with a preset override, manifest hashes could remain stale, causing false-positive "modified since installation" failures in
integration upgrade.Expected behavior: manifest hashes should be re-synced after registration writes so normal upgrades do not fail on untouched user projects.
Reproduction
init --integration claude).speckit.tasks.integration switch codex..specify/integrations/codex.manifest.jsonhash for.agents/skills/speckit-tasks/SKILL.mdwith on-disk bytes.integration upgrade codexwithout--force.The issue report included a complete Python repro script and expected/actual output.
Suspected Code Paths
src/specify_cli/integrations/command_switch.py:404— calls_resync_manifest_after_registration(...)after preset/extension re-registration, explicitly covering post-registration hash refresh.src/specify_cli/integrations/command_switch.py:380-389— registers extensions/presets before the resync call; this is the formerly vulnerable ordering if resync were absent.src/specify_cli/integrations/_helpers.py:535-550—_resync_manifest_after_registrationdocstring and logic explicitly describe this false-positive scenario and mention switch/use handling.src/specify_cli/integrations/command_use.py:75—integration usealso performs_resync_manifest_after_registration(...)after registration.tests/specify_cli/integrations/test_command_switch.py:31— regression testtest_switch_syncs_manifest_hash_for_preset_overridevalidates switch now records preset-final bytes and allows subsequent upgrade.Root Cause Hypothesis
The reported root cause is credible historically: saving manifest hashes before preset registration can stale tracked hashes when registration rewrites managed files. In the current codebase, that gap appears addressed by a dedicated post-registration manifest resync in
switch(anduse), plus targeted regression tests tied to #5078. Confidence: high that the specific bug report no longer reflects current behavior on main.Proposed Remediation
Preferred: No new code change from this triage. Treat this issue as no longer actionable on current main because the fix path and regression tests are already present. If maintainers need release bookkeeping, close as fixed by existing changes and/or link the fixing PR/commit.
Alternatives (optional):
switch/useresync behavior and associated tests there (trade-off: release branch churn and compatibility validation).Files likely to change:
Tests to add or update:
test_command_switch.pyand related integration tests.Risks & Considerations
Open Questions