fix: preserve .env overrides during git directory sync

[kmendell]

Checklist

• This PR is not opened from my fork’s main branch
• All new user-facing strings are translated via Paraglide (m.*())

What This PR Implements

Fixes: #2476

Changes Made

Testing Done

AI Tool Used (if applicable)

Additional Context

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Greptile Summary

This PR fixes a bug (issue #2476) where .env overrides edited in Arcane were silently wiped on every git directory sync because .env was being raw-written from the git payload instead of being routed through the three-file override merge (gitEnvContent → .env.git, project.env, .env).

• Core fix (gitops_sync_service.go): partitionReservedRootEnvFilesInternal splits the git payload so .env is captured as gitEnvContent (not written directly), then applyGitSyncEnvToDirInternal runs the same three-file merge that single-file sync uses. A companion filterReservedRootEnvFilesInternal drops .env from the old tracked-files list so CleanupRemovedFiles does not treat it as "removed by git" and delete the live-copied stage .env before the merge step reads it (addressing the migration case).
• Permission-locked env files (env.go, project_service.go): readOptionalProjectFileInternal now returns an unreadable flag for os.ErrPermission; WriteManagedEnvFile skips writes to locked files rather than aborting the sync.
• Lenient compose validation (project_service.go, load.go): validateComposeContentForUpdate gains a lenient bool parameter; git sync paths now tolerate undefined ${VAR} references that would previously fail with typed-decode errors during validation.

Confidence Score: 5/5

Safe to merge — the change is well-scoped to the directory sync path, backward-compatible via the legacy .env filter, and covered by three new regression tests.

The two concerns flagged in the previous review are both addressed: legacy sync.SyncedFiles entries containing .env are filtered before CleanupRemovedFiles sees them, and reserved-file drops from the git payload now emit slog.Warn entries. No new correctness issues were found after tracing the staging flow, the envContentChangedInternal signal, and the permission-locked skip path end-to-end.

No files require special attention.

Comments Outside Diff (2)

1. backend/internal/services/gitops_sync_service.go, line 87-107 (link)

   Silent drop of reserved files from git payload — no warning logged

   partitionReservedRootEnvFilesInternal drops .env.git, project.env, and .env.global from the git payload without emitting any log entry. Every other "skip" in this PR (permission-locked reads in readOptionalProjectFileInternal, seedStageEnvFromCandidateDirInternal, WriteManagedEnvFile) logs a slog.Warn. A git repo that accidentally commits .env.git or project.env — or intentionally commits .env.global (which was previously raw-written) — will have those files silently dropped with no trace in the logs, making the behavior change invisible to operators.

   Prompt To Fix With AI

   This is a comment left during a code review.
   Path: backend/internal/services/gitops_sync_service.go
   Line: 87-107
   
   Comment:
   **Silent drop of reserved files from git payload — no warning logged**
   
   `partitionReservedRootEnvFilesInternal` drops `.env.git`, `project.env`, and `.env.global` from the git payload without emitting any log entry. Every other "skip" in this PR (permission-locked reads in `readOptionalProjectFileInternal`, `seedStageEnvFromCandidateDirInternal`, `WriteManagedEnvFile`) logs a `slog.Warn`. A git repo that accidentally commits `.env.git` or `project.env` — or intentionally commits `.env.global` (which was previously raw-written) — will have those files silently dropped with no trace in the logs, making the behavior change invisible to operators.
   
   How can I resolve this? If you propose a fix, please make it concise.

   Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!

   

2. backend/internal/services/gitops_sync_service.go, line 1711 (link)

   Preserve migrated env
   When an existing directory sync was created before this change, sync.SyncedFiles contains .env; this call now compares it to syncedFiles after .env has been filtered out, so CleanupRemovedFiles deletes the copied live .env from the stage before applyGitSyncEnvToDirInternal can read it. With no prior .env.git/project.env, the merge falls back to the git .env and loses the Arcane-edited value during the first sync after upgrade.

   Rule Used: What: When implementing a feature, modify and reus... (source)

   Prompt To Fix With AI

   This is a comment left during a code review.
   Path: backend/internal/services/gitops_sync_service.go
   Line: 1711
   
   Comment:
   **Preserve migrated env**
   When an existing directory sync was created before this change, `sync.SyncedFiles` contains `.env`; this call now compares it to `syncedFiles` after `.env` has been filtered out, so `CleanupRemovedFiles` deletes the copied live `.env` from the stage before `applyGitSyncEnvToDirInternal` can read it. With no prior `.env.git`/`project.env`, the merge falls back to the git `.env` and loses the Arcane-edited value during the first sync after upgrade.
   
   **Rule Used:** What: When implementing a feature, modify and reus... ([source](https://app.greptile.com/ofkm/-/custom-context?memory=0983d2ab-8ef9-4463-85d5-a790cefce423))
   
   How can I resolve this? If you propose a fix, please make it concise.

   

_{Reviews (3): Last reviewed commit: "fix: preserve .env overrides during git ..." | Re-trigger Greptile}

[kmendell]

• fix: preserve .env overrides during git directory sync #3095 👈 (View in Graphite)
• main

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