[Bug]: integration switch leaves the manifest out of date when a preset overrides a core command #5078

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.