A GUI app's config is permanently dirty in `chezmoi status`

Symptom. chezmoi status shows MM on an app’s config file every time you look, even when you changed nothing. Running chezmoi apply “fixes” it, then it comes back after the app runs. Worse, bootstrap (which runs chezmoi apply --force) silently reverts real in-app settings changes along the way.

Root cause. Two writers on one file. The app owns and rewrites its config, and a statically chezmoi-managed copy fights it. LinearMouse is the sharpest case: it stamps "$schema": "https://schema.linearmouse.app/<app version>" into the file, so the file goes dirty on a timer — every app update produces a diff with no setting change behind it. That trains you to ignore the dirty status, which is exactly when a real reverted setting slips past.

Confirm.

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chezmoi diff ~/.config/linearmouse/linearmouse.json
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# -  "$schema" : ".../0.11.3"      <- what the app wrote
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# +  "$schema" : ".../0.11.2"      <- what apply would force back

Fix. Don’t let chezmoi manage app-owned configs. Use the apply/sync split (install/linearmouse.sh, install/claude-desktop.sh, install/codex-desktop.sh): the tracked source lives under install/<app>/, apply merges it into the live file live-first so app-owned keys survive, and sync captures in-app changes back. For LinearMouse specifically the tracked source omits $schema entirely, so only genuine setting changes ever diff.

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bash install/linearmouse.sh sync    # capture in-app changes → repo
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bash install/linearmouse.sh         # push repo settings → app (default: apply)

Adding a new app to this pattern means deleting its home/ chezmoi source (chezmoi then leaves the live file alone), adding the script, and wiring a DF_DO_* flag in bootstrap.sh.