Adds ParentID and MergeParents to agent.CommitOpts. When ParentID is 0, Agent.Commit auto-resolves the current trunk tip and uses that as the parent — matching `fossil ci`'s default behavior. On an empty repo (BranchTip returns sql.ErrNoRows), the resolution falls through to 0 and the commit is a legitimate orphan root (the first commit).

Before this fix, agent.Commit always passed ParentID=0 to libfossil, producing P-card-less manifests. Every commit became its own root, fragmenting the timeline and breaking trunk-based development for downstream consumers (notably bones).

Tests added: - TestAgent_Commit_ChainsOntoTrunkTipByDefault — two consecutive Commit calls produce a chained pair with linked Parents. - TestAgent_Commit_ExplicitParentIDOverride — caller-supplied ParentID is used verbatim.

The hub-leaf e2e test (sim/hub_leaf_test.go) was reading by "trunk" tip on the hub; switched to reading by the explicit RevID returned from Agent.Commit so the test exercises the transport contract (file lands on hub) without coupling to branch-tip resolution semantics on the hub side after sync — which appears to be a separate concern worth its own investigation.

Closes #125 check-in: 82e4b0075d user: [email protected] tags: trunk