agent.Commit passed opts.Files straight through to libfossil.Commit, which emits a partial manifest containing only the supplied subset. Parent files not in opts.Files were silently dropped — bones' multi-slot workflow (each slot commits only its own paths on a linear trunk chain) materialised only the last slot's files into git, every prior slot's work lost. Bug chains to libfossil#30, but EdgeSync can shield consumers regardless of upstream's resolution.

opts.Files now reads with `fossil ci` semantics — "files this commit changes." A new mergeWithParent helper enumerates the parent's F-cards, overlays supplied files (supplied wins by name), and hands the full set to libfossil.Commit. Inherited files preserve the parent's Perm; supplied files get libfossil's default (agent.FileToCommit has no Perm field today). parentID==0 stays an orphan root.

Two regression tests: - TestAgent_Commit_PreservesParentFiles — disjoint paths (alpha, bravo) on a linear chain. Both must surface at trunk's tip. - TestAgent_Commit_SuppliedFileOverridesParent — same-name supplied content must win over parent's.

Tests verify against BranchTip + ReadFile directly. a.Read can't be used because libfossil ResolveVersion("trunk") goes through the sym-trunk singleton tag, which libfossil.Commit doesn't propagate forward; only the first commit on trunk is reachable that way. Orthogonal to #152; flagging separately.

Closes #152

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> check-in: 7f0fbfa6ef user: [email protected] tags: trunk