The --update runbook's Step 9 stamped the entire detected corpus into the
manifest, so a semantic file (doc/paper/image) whose chunk failed or was omitted
was recorded as done and never re-queued on the next update — losing its content
permanently. The runbook now builds the manifest the way the library extract
path does: cli._stamped_manifest_files stamps only files that actually produced
nodes/edges/hyperedges, dispatched-but-empty files have their stale hash cleared,
and scan_corpus drops newly-excluded in-root rows.
Applied to the Claude, Aider, and Devin skill bodies and the shared update
reference; all 134 artifacts regenerated. gen.py gains a sanctioned monolith-
diff predicate for the new stamping lines.
The skill runbooks called save_manifest(...) with no root=, so manifest keys
were stored as absolute paths (e.g. /Users/.../main.go). Cloning or moving the
repo then broke `graphify --update`: detect_incremental matched none of the
cached keys, so the entire corpus re-extracted (and the report showed ghost
nodes). The native `graphify extract`/`update` CLI already passed root=target;
the agent-executed runbooks did not.
All four runbook call sites now pass root='INPUT_PATH', relativizing manifest
keys to the scan root (portable forward-slash form, per save_manifest's #777
support): the lean-core skill.md Step 9, the shared --update reference, and the
Aider/Devin monoliths.
The monolith edit is registered as a new sanctioned change-class
(_is_manifest_root_fix_line) in the round-trip guard, mirroring how the #1392
runbook fixes were sanctioned. Regenerated + blessed all artifacts; added a
regression test asserting every shipped runbook threads root= into save_manifest.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Closes the non-crash tier of #1392 in the Claude-path skill fragments:
- #6/#7: build_from_json/build_merge now take directed=IS_DIRECTED in Step 4, Step 5 rebuild, and the --update merge/diff, with prose telling the agent to substitute IS_DIRECTED like INPUT_PATH (a --directed run no longer silently rebuilds undirected and collapses reciprocal edges)
- #10: semantic extraction only flattens document/paper/image, not code (AST already covers code) so subagents stop re-reading every source file
- #12: .graphify_cached.json is deleted on a cache miss so Part C never merges a stale cache from a prior run
- #11: --update now transcribes changed video files and moves transcripts to documents before the semantic pipeline
- #4/#5/#23: transcribe writes via write_text (no shell redirect), uses GRAPHIFY_WHISPER_MODEL/PROMPT env, status to stderr
- #2/#3: add-watch and exports use $(cat graphify-out/.graphify_python) explicitly; MCP Desktop config documents the absolute interpreter path
- #21: extraction-spec example id namespaced (auth_session_validatetoken)
- #22: query term split keeps tokens >= 3 chars
aider/devin monoliths are pinned by the roundtrip invariant and excluded; their own Step 1 already instructs replacing python3 with the resolved interpreter.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Five fixes in the skillgen fragments (re-rendered): chunk paths now derive from
cwd to match where Part C globs (a non-cwd scan produced "no nodes"); the
code-only fast path writes an empty .graphify_semantic.json so Part C doesn't
FileNotFoundError; --cluster-only relies on the self-contained CLI instead of
re-running Steps 5-9 against deleted intermediate files; and Step 4 runs the
zero-node guard before any write and only writes GRAPH_REPORT.md / analysis when
to_json actually persisted the graph (honoring the #479 shrink-guard).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
After #1361 added root= to the --update build_merge call, build_merge's prune
(which runs after the merge) began matching freshly re-extracted changed-file
nodes and deleting them — a regression in 0.8.41 where --update on a changed
file wiped its nodes. This drops `changed` from prune_sources (replace-on-
re-extract from #1344 already reconciles changed files), passes root= to the
full build's build_from_json so its node-key base matches the update side, and
pins the extraction-spec source_file to the verbatim path so the two runs never
drift. Re-blessed skillgen expected/ snapshots.
Co-Authored-By: RelywOo <RelywOo@users.noreply.github.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The /graphify --update runbook called build_merge with absolute prune_sources
but no root=, so _norm_source_file never relativized them to match the graph's
relative source_file values. Nothing was pruned and changed/deleted files left
ghost nodes that compounded on every incremental update. Fix the shared skillgen
fragment to pass root='INPUT_PATH' and re-render all platform artifacts.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Three-part fix:
dedup.py: Pass 1 exact-merge now skips nodes with an empty source_file.
Previously all no-source_file nodes with the same label landed in one
bucket and were merged, destroying distinct symbols (third-party deps,
standalone functions) that happened to share a short name.
update.md (skillgen + all 13 host variants): the --update merge now
passes both deleted AND changed files to prune_sources, mirroring what
watch._rebuild_code already does correctly. Old nodes for re-extracted
files are pruned before fresh AST is inserted — no fuzzy reconciliation
needed, no cross-file collapse possible.
export.py: anti-shrink guard message now names fuzzy dedup as a
possible cause (not only "missing chunk files"), and advises a full
rebuild as the safe recovery path.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
All-platform progressive-disclosure skill split + generator (addresses #1106).
Splits each platform's skill into a lean core (~615 lines, full default pipeline inline) + on-demand references/, generated from a single source via tools/skillgen with a CI/pre-commit drift gate. 13 hosts split, aider/devin stay monoliths. Also fixes the stale bare-path bugs across the previously hand-maintained variants and moves the always-on blocks into packaged markdown.
Verified: all 5 generator guards pass, byte-verbatim load-bearing slices, lean cores self-sufficient on the default path across all 13 split hosts, references gated to non-default branches, description preserves the graphify-out-query-first clause. Supersedes #1119 (Claude-first subset).
Known follow-up applied on top: harden _always_on() against a missing packaged file so a partial install can't brick the CLI.
safishamsi