Function apply_install 

pub fn apply_install(plan: &InstallPlan, root: &Path) -> Result<FileManifest>

Applies an install plan into root, copying files and recording what was written.

root is the caller-supplied profile/loader root. Parent directories are created as needed. Files tracked as none (shared config) are written only if absent and are never recorded, so a user’s edits survive reinstalls and they are never auto-removed; all other files are (over)written and recorded in the returned FileManifest (paths relative to root).

The apply is all-or-nothing: if any entry fails, every file this call created is removed before the error is returned — along with any directory tree this call newly created (now left empty) — so a partial install leaves root as it found it, with no untracked files or empty directories behind.

For a none-tracked (shared config) destination that already exists — a regular file or a symlink the user planted — the entry is skipped and left untouched, so a user’s edits (or their symlinked config) survive. For a tracked destination, a symlink already sitting there is refused rather than followed, so a pre-planted leaf link cannot redirect the write. This is best-effort: it inspects the final path component only (not symlinked parent directories) and is not race-free against a concurrent attacker mutating root mid-install.