reconcile

Run dt reconcile to surface drift between the graph and the current state of the code. Read-only — never fixes anything automatically. The user decides what to apply afterwards via targeted dt_update_node calls.

Steps

1. Determine scope. If $ARGUMENTS contains a git revision (e.g. HEAD~5, main, a sha), pass it as --since; otherwise do a full scan.

2. Run:

   dt reconcile --json [--since <rev>]
   

   The command exits with code 1 if there is drift, 0 if clean. Either way, parse the JSON from stdout.

3. Summarize in this shape:

   ## DomainTome reconcile (<scope>)
   
   Scanned: N nodes with source_ref.
   Warnings: <if any, one per line>
   
   **dead_refs** (N): source_ref points at a file that no longer exists.
     - node-id-1 → path:line
     - node-id-2 → path:line
     ...
   
   **stale** (N): last_verified_at older than <threshold> days.
     - node-id  (last verified D days ago)
   
   **never_verified** (N): has source_ref but never marked verified.
     - node-id
   
   Verdict: <one sentence>
   

4. Suggest concrete next actions for each finding:

   • dead_refs: "Decide per node — either delete (status='archived'), update source_ref to the new path, or confirm the concept still exists even though the file moved."
   • stale: "Re-verify by inspecting the referenced code, then dt_update_node(id, metadata_patch={'last_verified_at': '<today>'})."
   • never_verified: "After a bootstrap, mark each node verified once you've checked it corresponds to the code."

5. Do not write to the graph. If the user asks for fixes, then write — but each write requires an explicit user decision per node.

Rules

• Never fabricate counts. If reconcile says 0 dead_refs, that is the number. Do not invent findings to look helpful.
• never_verified is lower priority than stale. If both lists are large, lead with dead_refs and stale.
• If the report includes warnings (e.g. not a git repo), surface them verbatim.