fix: recognize batch-existing.json in incremental merge (graph no longer collapses to changed files)

[rodcon]

Problem

The incremental /understand path collapses the knowledge graph down to only the changed files.

skills/understand/SKILL.md (Phase 2, "Incremental update path") writes the pruned prior graph to batch-existing.json and states:

4. Run the same merge script - it will combine batch-existing.json with the fresh batch-*.json files

But merge-batch-graphs.py discovers batch files and filters them with:

m = re.match(r"batch-(\d+)(?:-part-(\d+))?\.json", f.name)

batch-existing.json has no numeric index, so it does not match, is appended to unrecognized_batch_files, and is skipped at load:

unrecognized_set = set(unrecognized_batch_files)
...
if f.name in unrecognized_set:
    continue

Result: on every incremental update, all retained nodes/edges from the prior graph are dropped and the assembled graph shrinks to just the files that changed in that commit. The script prints a generic "unrecognized filenames will be DROPPED" warning, but the file it is dropping is the one the skill's own incremental path is documented to produce.

Fix

Recognize batch-existing.json explicitly and sort it first (key = -1) so the fresh per-file batches still override it during dedup (the merge keeps the last occurrence per node id):

• _batch_sort_key returns -1 for batch-existing.json so it loads before the numbered batches.
• The grouping loop handles batch-existing.json as a valid batch instead of marking it unrecognized.

Minimal change, one file, no behavior change for full analysis or for the existing batch-<N>.json / batch-<N>-part-<K>.json handling.

Verification

Standalone repro against the patched script:

• batch-existing.json = files a, b, c + an imports edge (the retained prior graph)
• batch-0.json = changed file d

	assembled nodes	edges
before	file:d.py only (1)	0
after	file:a.py, file:b.py, file:c.py, file:d.py (4)	1

Dedup still works (fresh batch overrides existing for a changed file, because existing loads first).

Notes

Happy to add a test in whatever harness you prefer for the Python scripts (I didn't see an existing pytest setup alongside the vitest suites - let me know and I'll wire one up).