How your files are handled

By default CapsCode uses a git snapshot, not a live mount:

1. Your repo's HEAD is cloned into a private container volume; uncommitted changes are carried in as a WIP commit.
2. Untracked files are excluded by default (keeps .env, tokens, and local junk out of the capsule and out of the tool's context). Add specific ones with --include.
3. Remotes and credential helpers are stripped; the capsule gets a temporary git identity.
4. On an interactive exit, CapsCode summarizes changed files and offers to save them under a clearly labeled auto-generated branch, apply them to the current folder, review the diff, continue in the capsule shell, or discard them.
5. Automated and batch runs safely save changes to an auto-generated CapsCode branch. The host working tree is never changed automatically. If the capsule made no changes, CapsCode exits without showing a handoff menu.

--history full is the default. --history shallow gives the capsule a depth-one clone; --history redact-authors creates a synthetic history with no original commits. In Git mode, capscode sync <box> saves work on a capscode/<id> branch. If changes touch hook or runner files, CapsCode keeps the change set on that branch instead of applying it to the host worktree.

Choosing Apply changes to this folder first preserves the generated recovery branch and then applies the capsule patch. The current branch and Git index are left unchanged.

--mount (or workspace.mode = mount for one-shot runs; boxes need create --mount) is a convenience mode that bind-mounts the project read-write instead (faster, full git metadata visible to the tool, but the agent can modify host files directly, with no copy-back review standing between it and your files — use deliberately). capscode sync <box> reports itself a no-op in mount mode, since there is nothing to copy.

Non-git directories work too. CapsCode snapshots the folder host-side (the capsule sees no .git at all), quiesces the capsule before capturing changes, and then offers to apply clean, non-conflicting files back to your folder — with per-file conflict detection against the session baseline, backups of anything overwritten, and a durable staging copy for whatever it declines to touch. Non-interactive runs never write to your folder.

capscode sync <box> and capscode rm <box> can copy a non-git workspace back too. Sync stops a running box to capture a consistent snapshot; after sync, enter it again with capscode <box> or run capscode resume <box> to rebuild it around the workspace. A box removed with rm does not take uncopied work with it. Each handoff round retires the previous one into previous-handoff.<n> rather than overwriting it — staging holds what was not applied and the backup holds host files that were, so either may be the only copy of something. Nothing is pruned automatically.

Non-Git copy-back also classifies what it imports. Nothing under .git/ is ever written to your host, and files your host would execute out of repo content — .husky/, .githooks/, .envrc, .pre-commit-config.yaml, lefthook.* — are reported and skipped rather than applied, so a capsule cannot plant something your next git commit runs.