graph_diff keyed undirected edges by their sorted endpoints, so a call
that reversed (a->b became b->a) dropped out of the --update summary.
When both snapshots carry _src/_tgt and they differ, the edge is now
reported as one removed and one new edge, with source/target taken from
the markers. Graphs without the markers diff as before.
The skill's diff step loaded the old graph.json with a plain
node_link_graph call, which drops the stored direction, so it now uses
paths.load_node_link_graph (#4066/#4088). Skills regenerated with
skillgen, and the aider/devin monolith round-trip allows the changed
lines.
Closes#4067
Co-Authored-By: Grok Bot <noreply@x.ai>
(cherry picked from commit 917fab9fbb)
The split-host runbook told the agent to skip to Part C when every doc,
paper and image hit the semantic cache. Part C reads
.graphify_semantic.json unconditionally and only the Step B3 merge writes
it, so a second run on an unchanged mixed corpus failed with
FileNotFoundError; writing an empty file instead dropped every cached node.
The all-cached case now skips B1/B2 but still runs B3. Step B0 also clears
.graphify_chunk_*.json before dispatch: B3 merges every chunk on disk, and a
leftover from an interrupted run would otherwise be merged as fresh.
The aider and devin monoliths keep the old sentence; they are pinned to the
v8 baseline by --monolith-roundtrip.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
(cherry picked from commit bab1bb2775)
Completes #3742: the Step 1 fix closed the .graphify_root shell line, but
the progressive-disclosure add-watch reference still passed the raw,
agent-substituted INPUT_PATH placeholder unquoted into a bash command
($(cat .graphify_python) -m graphify.watch INPUT_PATH), the same
injection class - a scan root like $(...) / ; rm ... would execute.
The watcher targets the folder graphify already extracted, so read the
trusted graphify-out/.graphify_root that Step 1 resolves (the same
sidecar pattern this reference already uses for .graphify_python)
instead of re-substituting the untrusted placeholder. Regenerated all
14 host add-watch artifacts + expected/ snapshots; monolith-roundtrip
and always-on-roundtrip stay green (cores untouched).
The identical sink in the aider/devin monolith cores is tracked
separately (editing a core requires a gen.py sanctioned-diff).
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Step 1's own bash and PowerShell fragments both built a command whose
literal text was the resolved scan path, substituted verbatim by the
agent following the instructions before that line ever ran. The bash
form, echo dollar paren cd INPUT_PATH and pwd close paren, still
expands a command substitution even inside the outer double quotes,
and the cd itself was entirely unquoted; the PowerShell form passed
INPUT_PATH as a bare unquoted argument to Resolve Path, exposed to the
same class of problem through a stray semicolon or pipe. A path drawn
from an untrusted source, a malicious readme's suggested command, a
copied value from an untrusted page, executed as code the moment this
line ran, before any Python was ever reached.
Both now capture INPUT_PATH through a construct their own interpreter
guarantees performs no expansion at all: a quoted bash heredoc for the
posix form, a single quoted PowerShell here string for the windows
form. The raw text reaches Python (respectively Resolve Path) only as
inert data on standard input, never as source the shell itself
parses. Verified for the posix form by actually executing the
extracted Step 1 block with a malicious substituted value and
confirming no injected command runs; the PowerShell form could not be
executed in this environment (no interpreter available to install
without an interactive credential prompt), so it was written using
well established, unambiguous here string syntax and reviewed
carefully rather than run.
As a side effect of no longer building the path through an unquoted
cd, a legitimate path containing a space is now handled correctly
too, and a nonexistent path now fails the whole step loudly instead
of silently continuing past a swallowed cd error.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh
(cherry picked from commit 9a7e5d0a51)
Windows PowerShell 5.1 writes a UTF-8 BOM, so the .graphify_root marker it produced carried
a leading BOM that Python's utf-8 decode kept as U+FEFF; .strip() left it in, breaking the
post-commit rebuild (WinError 123) and silently mis-rooting _infer_merge_root. Write the
marker BOM-less from PowerShell (WriteAllText + UTF8Encoding $false) and read the marker
with utf-8-sig at the reader sites so already-broken installs recover too.
The Windows skill variant had a PowerShell Step 1 but its later steps came
from the shared core fragment as bash-only shell (cat-piped interpreter
invocations, rm -f, find -delete). The skillgen renderer now translates the
composed core to PowerShell for powershell-shell platforms (here-string
interpreter invocations, Remove-Item cleanup); POSIX skills are unchanged
and step / #2490 parity is enforced by a generator check. Not a regression
from 0.9.35 (skill files were unchanged between 0.9.34 and 0.9.35).
Thanks @tannermosher2015-debug.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#2486 (thanks @adminwat): normalize dict-shaped hyperedge members to ids
(or drop with a warning) so a malformed hyperedge can't abort a completed
merge with a TypeError.
#2484 (thanks @sortakool; approach from @oleksii-tumanov's #1691):
merge-graphs relabels hyperedge member ids and ids with the repo prefix,
unions both inputs' hyperedges instead of clobbering, and writes both
persistence slots.
#2485 (thanks @sortakool): build_from_json reads hyperedges from the
top-level and nested slots; a full validation wipeout is reported loudly.
#2490 (thanks @PapiScholz): the skill Step-5 flow passes curated
community_labels to to_json, so graph.json ships community_name.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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 semantic cache keyed entries on sha256(file content + path) alone, with
no component for the extraction prompt that produced them. After an upgrade
that changed the prompt, every unchanged file was a cache hit and replayed
the older prompt's extraction: the run exited 0, cost.json looked cheap, and
the graph silently carried two prompt generations side by side. The reporter
saw 506 of 512 docs replay an older vintage on a rebuild they expected to be
cold; deleting the whole cache was the only workaround.
output, and invalidating them on every release would re-bill extraction for
unchanged files. Fingerprinting the prompt itself keeps both properties:
entries survive releases that don't touch the prompt, and invalidate only
when it actually changed.
Semantic entries now live under cache/semantic/p{fingerprint}/, mirroring the
AST cache's v{version}/ layout. Both extraction paths pass their prompt: the
Python/CLI path from llm.py's _EXTRACTION_SYSTEM (shared by every backend),
and the skill path via a new prompt_file argument in Step B0/B3 naming the
references/extraction-spec.md the subagents were handed. The fingerprint
normalizes line endings so a CRLF checkout isn't mistaken for a new prompt.
Pre-existing entries predate fingerprinting and have unknowable vintage, so
they are still served rather than re-billing a whole corpus on upgrade — but
check_semantic_cache now warns with the count, turning "no signal at all"
into a visible one. merge_existing refuses to fuse such an entry into a
current-vintage write, which would mix two prompts inside one entry and then
attest the result to a prompt that produced half of it.
Old-fingerprint entries are pruned by liveness only, never swept wholesale
the way stale AST versions are: two hosts with different prompts (verbose vs
compact extraction-spec) can share one graphify-out/, and a wholesale sweep
would have each run delete the other's entries and re-bill on every
alternation. prune/clear/cached_files glob recursively so fingerprinted
entries can't become unprunable orphans (the #1527 failure mode).
The two monolith skills (aider, devin) inline their prompt instead of
shipping a spec sidecar and stay on the unfingerprinted path for now.
Step 1's POSIX interpreter probe ran `uv tool run graphifyy python -c ...`,
but the graphifyy package exposes its executable as `graphify`, so uv treated
`python` as a missing `graphifyy` command. The probe failed, and `2>/dev/null`
swallowed uv's "use --from" hint, leaving PYTHON on a system interpreter that
does not have graphify installed. The probe now runs
`uv tool run --from graphifyy python -c ...`.
Applied to the skillgen source fragments (shell/posix.md and the aider/devin
monoliths) and regenerated all skill*.md; added a sanctioned monolith-diff
predicate and re-blessed the expected/ snapshots. The PowerShell path was
already correct (it probes the venv python.exe directly).
Reported and originally patched by @mohammedMsgm in #1736.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The Usage block's bare `/graphify` comment read "full pipeline on current
directory -> Obsidian vault", contradicting Step 6 (HTML viz always; Obsidian
vault only when --obsidian is explicitly given). The comment predated the
opt-in change and told agents a bare /graphify produces a vault. It now reads
"full pipeline on current directory (HTML viz; add --obsidian for a vault)".
Fixed at the skillgen source (fragments/core/core.md + the aider monolith
override), added a sanctioned-diff predicate so the monolith round-trip guard
allows the change, and re-blessed the expected/ snapshots. Every generated
skill-*.md now carries the corrected comment; the only content change across
all rendered files is this one line.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1635: the windows skill variant declared `name: graphify-windows`, but
`graphify install --platform windows` writes it to ~/.claude/skills/graphify/
SKILL.md and Claude Code requires the folder name to equal the frontmatter
`name` — the suffix broke discovery. platforms.toml now sets name = "graphify"
(regenerated + re-blessed).
#1646: the OpenCode (and Kilo) plugin prepended its reminder with `&&`, which
Windows PowerShell 5.1 rejects as a statement separator, breaking the first
bash command of every session. Switched to `;` (valid in PowerShell 5.1, Bash,
POSIX).
#1657: the GRAPH_REPORT.md "Import Cycles" section printed "None detected" on
documents-only corpora where imports don't exist — now gated on code nodes /
import edges being present. The other two items in that issue (mojibake in
manifest/report, stdout encoding) are already handled on current v8: both files
are written UTF-8 and main() reconfigures stdout/stderr to UTF-8.
Full suite: 2909 passed, 3 skipped.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The query reference doc's inline vocab-harvest / fallback-search snippets used
bare Path(...).read_text()/write_text(), which on Windows (default cp1252)
crash with UnicodeEncodeError on the cross-language corpora the doc itself
demonstrates (Cyrillic labels like обработчик). Add encoding="utf-8" to all
five sites in the skillgen source fragment and regenerate; blessed expected/,
skillgen --check + --monolith-roundtrip green.
Scoped to the concrete reproduced crash; the larger #1619 findings (the
Windows .exe interpreter-guard rewrite, INPUT_PATH backslash guidance, BOM
handling) are a separate skill-template pass.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#1586: the skill's interpreter-detection allowlist rejected any shebath path
with a char outside [a-zA-Z0-9/_.-], so Homebrew's versioned python@3.13 path
was skipped and detection fell through to a bare python3 without graphify.
Allow @ in the skillgen source fragments (core/devin/aider/posix), regenerate
all skill artifacts, and register the change as a sanctioned monolith diff.
Injection chars (; $ ( etc.) are still rejected.
#1606: graphify merge-graphs crashed with an unhandled NetworkXError when
inputs disagreed on directed/multigraph. _to_simple only converted MultiGraph,
leaving a DiGraph to fail compose. Normalize every input to a plain undirected
Graph (the merged cross-repo view is undirected anyway).
Also confirmed on v8: `graphify kilo install` (#1605) works (reporter was on an
older version), and `pip3 install graphifyy` failing on macOS (#1585) is a
broken Homebrew Python 3.14 / pyexpat env, not a graphify issue — pip crashes
in its own vendored distlib before graphify is touched.
skillgen --check / --monolith-roundtrip / --schema-singleton all green; shell
smoke accepts python@3.13 and still rejects `; rm -rf /` and `$(evil)`. Full
suite 2789.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Generated install/skill guidance told agents to invoke a literal `skill`
tool with `skill: "graphify"`, which is host-specific and not valid in
every environment. The always-on AGENTS fragment, packaged artifact,
expected snapshot, and _skill_registration() output now use host-generic
wording: "use the installed graphify skill or instructions". Also decodes
skillgen git blob reads as UTF-8 for Windows and replaces stale English
code-block examples in the translated READMEs.
The always-on roundtrip guard deliberately freezes the v8 baseline, so an
intentional wording change would otherwise fail it. Rather than only
patching the pytest mirror (which left the blocking CLI guard
--always-on-roundtrip red, as the original PR did), this adds an explicit,
reviewable ALWAYS_ON_SANCTIONED_EDITS registry: the guard applies the
approved old->new substitution to the baseline before the byte-for-byte
compare, so this exact sentence is allowed while any other drift still
fails. CLI guard and pytest test now agree and CI passes.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
These were committed before .gitignore included the .DS_Store rule, so
gitignore never removed them from tracking. Untrack them (they remain
on local disk, just leave git) — the existing .gitignore rule keeps
them out going forward.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
BREAKING node-ID format change. The stem that prefixes every node id was the
immediate parent dir + filename, so same-named files in different directories
collided into one last-writer-wins node and silently dropped graph content
(docs/v1/api/README.md and docs/v2/api/README.md both -> api_readme). The stem is
now the full repo-relative path (docs_v1_api_readme vs docs_v2_api_readme);
top-level files are unchanged (setup.py -> setup).
- extractors/base.py::_file_stem -> full path (as_posix; make_id collapses
separators). The two hand-copied stems (symbol_resolution, mcp_ingest) now
import the canonical one, so they can't drift again.
- llm.py system prompt + extraction-spec fragments aligned to the same rule,
fixing the #1509 AST<->LLM divergence (prompt used zero parent dirs -> ghosts).
Regenerated + blessed the per-host specs.
- build_from_json deterministically re-keys every non-AST node id from its
source_file via the new stem (and registers old-stem aliases), so a cached or
pre-migration semantic fragment carrying an old short id reconciles with the
AST node instead of spawning a ghost. The semantic cache is unversioned, so
this code-side re-key (not LLM prose) is what makes it survive the format change
with no re-bill. AST nodes are already canonical and skipped.
- Migration: existing graphs migrate automatically on the next build/update (the
re-key runs in build_from_json, including the whole graph fed back through
build_merge); `graphify extract --force` for a clean rebuild. Neo4j persisted
stores need a re-import; GraphML layouts go stale.
Full suite green (2505 passed); #1504 collision fixed and old-id fragments
re-keyed verified by smoke. Lands on v9 for review before a 0.9.0 release.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Hermes and the other AGENTS.md hosts (Codex, Aider, OpenClaw, Droid, Trae, ...)
run the graphify CLI directly and do not dispatch subagents. The Step 3 extraction
guidance only described the no-API-key path as "fall straight through to subagent
dispatch", so on `/graphify .` those agents had no path they could take, fixated on
the GEMINI/ANTHROPIC key language, and looped for minutes insisting on a missing key
before eventually proceeding (a pure-code corpus is AST-only and needs no key at all).
Step 3 now opens with a hoisted, host-agnostic statement -- graphify needs no API
key, never prompt for one, never block on one; code is AST-only; a code-only corpus
skips semantic extraction entirely -- and the no-key fallback now spells out a
terminal-only path (write the empty semantic file and continue, or extract content
inline) instead of assuming subagent dispatch.
Applied in the shared core fragment and in the aider/devin core variants, so all 16
skill bodies carry it; the aider/devin change is registered as a sanctioned
monolith-roundtrip diff. Regression test (test_extraction_states_no_api_key_required_
for_every_host) renders every host and pins the wording, ordering, and the
non-subagent fallback so this can't silently regress.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Both the agent (session start) and the post-commit hook can run reflect; the runs
are deterministic and idempotent, but back-to-back ones are wasted work. Add
`graphify reflect --if-stale`, which no-ops when LESSONS.md is already at least as
new as every input (the memory docs and the graph). The skill's session-start
guidance now uses `--if-stale`, so when the hook just refreshed the file the
agent's run costs almost nothing, while a skill-only install still refreshes
on demand.
New lessons_fresh() helper + 5 tests (mtime freshness in each direction, and the
CLI skip/run behavior). Regenerated per-host references + re-blessed expected/;
all five skillgen guards pass; full suite 2388 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A skill-only install (no `graphify hook install`) recorded outcomes via
save-result but never ran reflect, so LESSONS.md was never generated or
refreshed and the lessons never surfaced. The query reference now instructs the
agent to run `graphify reflect` itself at the start of graph work (cheap,
deterministic, no-op with no saved outcomes) before reading LESSONS.md. The
post-commit hook stays as a between-session freshness optimization, not a
requirement. Regenerated per-host references/query.md + re-blessed expected/;
all five skillgen guards pass; full suite 2383 passed.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Make the self-improving loop "just work" once graphify is installed:
- Skill: the query reference now tells the agent to read
graphify-out/reflections/LESSONS.md at the start of graph work (start from
preferred sources, skip known dead ends, see prior corrections) and to record
--outcome useful|dead_end|corrected (+ --correction) on save-result.
- Hooks: the post-commit and post-checkout rebuild bodies now auto-run reflect
after _rebuild_code — best-effort, only when graphify-out/memory/ holds saved
outcomes, and never fails the hook — so LESSONS.md refreshes on every rebuild
without a manual `graphify reflect`.
Regenerated the per-host references/query.md and re-blessed expected/; all five
skillgen guards pass (check, audit-coverage, schema-singleton, monolith-roundtrip,
always-on-roundtrip). Verified end-to-end: install hook, save-result --outcome,
commit a code change -> hook rebuilds and writes LESSONS.md with the outcome.
Full suite 2383 passed; ruff clean.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
`graphify install --platform agents` installs the skill to the generic
Agent-Skills locations: the spec's user-global ~/.agents/skills (global) and
./.agents/skills (--project) — the directories `npx skills` and spec-compliant
frameworks read. `--platform skills` is an alias. Previously that user-global
location was only reachable as an accidental side effect of the gemini-on-Windows
branch. Bare `graphify install` is unchanged (still single-platform claude/windows).
The platform is registered in tools/skillgen/platforms.toml (split, mirroring
amp's agents-md body) and rendered through the skillgen drift/coverage guards.
Since it is a post-v8 platform with no own v8 body, its --audit-coverage baseline
is amp's v8 body (the body it re-homes). The rendered skill body is byte-identical
to amp's; only the on-demand hooks reference differs (its own `graphify agents
install` wording).
The `graphify agents install` / `graphify skills install` subcommand is the
amp-twin: it also wires an AGENTS.md always-on section, keeping it honest with the
hooks reference it points at. The `--platform agents` path stays skill-only,
exactly as amp's `--platform amp` does.
Also: `skill-agents.md` added to package-data, and the wheel-packaging guard now
covers every platform's skill body (not just references/always-on), so a missing
skill body fails CI instead of only breaking install for real users.
Closes#1405. Implements #1432.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Two integrity improvements to the core skill runbook (rendered via skillgen):
1. Graph-health gate (new Step 4.5): runs diagnostics.diagnose_extraction
read-only after build, before labeling, and surfaces dangling/missing/
self-loop and same-endpoint-collapsed edges — the silent-corruption modes of
incremental updates and AST/LLM id mismatches. Never aborts.
2. Anchor the AST and semantic caches on the scan root (root/cache_root=
'INPUT_PATH') instead of the cwd, matching the CLI extract path
(ast cache_root=out_root, check/save_semantic_cache(root=out_root)) and
build_from_json/save_manifest (#1361 parity). Without this, running from a
cwd != scan root cold-misses the cache and can split AST vs semantic caches.
Source edited in tools/skillgen/fragments/core/core.md; artifacts + expected/
regenerated via 'python -m tools.skillgen' (+ --bless). Full suite green
(2229 passed); skillgen + cache suites green (80 passed).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The split-skill runbook passed '.' as report.generate's root argument in
Steps 4 and 5, so `/graphify /some/path` produced a report titled
"# Graph Report - ." regardless of the scanned directory. It now passes
'INPUT_PATH' (the Aider/Devin monoliths were already correct). Display-only:
no path written to graph.json or manifest.json was affected. Regenerated +
blessed the split-skill artifacts.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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>
The monoliths are hand-maintained single files frozen against a pinned pristine-v8 blob by the round-trip guard, so they were excluded from the 0.8.44 #1392 batch. Evolve the guard from a positional zip (line-count-exact, single-line-class allowlist) to a multiset diff that classifies every added/removed line against documented sanctioned change-classes, so the multi-line fixes can land while any unsanctioned drift still fails. Add predicates for the four fix classes and broaden the enum/chunk-cleanup predicates to match both the v8 and rewritten forms.
Both monoliths now: thread directed=IS_DIRECTED through every build_from_json call (a --directed run no longer collapses reciprocal edges), scope semantic extraction to document/paper/image, unlink a stale .graphify_cached.json on a cache miss, and run Step 4's zero-node guard before any write with the report/analysis gated on to_json persisting the graph (#1392).
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>
Completes the source_file convention fix begun in #1344 (build_merge
replace-on-re-extract) and #1361 (pass root= to build_merge in the --update
runbook). Two gaps still let the full build and incremental --update emit
different source_file bases for the same file, so the source_file-keyed replace
missed and duplicates accumulated:
1. extraction-spec(.md/-compact.md): the subagent's source_file slot was an
unpinned "relative/path", so it invented a base per run (and the node id,
derived from the same path, drifted too). Pin it to the verbatim FILE_LIST
path so _norm_source_file(root) canonicalizes every run identically.
2. core.md: the full build called build_from_json WITHOUT root=, so #1361's
update-side root= had no matching base on the full-build side. Pass
root='INPUT_PATH' at both sites (Step 4 export, Step 5 report) so the full
build and --update relativize to the same base.
update.md prune_sources = deleted only. Changed files are replaced by build_merge
(#1344); once root= aligns the bases, leaving `changed` in prune_sources would
delete the freshly re-extracted nodes.
Engine (build.py) unchanged. Regenerated all skill artifacts via
tools/skillgen/gen.py. Adds test_build_merge_root_collapses_convention_drift.
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>
The query skill was split across two fragments so no platform got both
capabilities: Claude had the vocab/IDF query-expansion step but no fallback if
the CLI was unavailable; every other platform had the inline NetworkX fallback
but the weaker raw-question matcher. Merge into one unified query reference +
stub (Step 0 expansion -> CLI traversal -> inline NetworkX fallback, plus
path/explain inline) shipped to all hosts. Remove the query_variant enum, its
toml field, and the _CLI_ONLY_QUERY_HEADINGS coverage-audit exemption. Re-render
all skill artifacts and re-bless expected/. skillgen check/audit-coverage/
monolith-roundtrip/schema-singleton all pass. Refs #1325.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The no-push 'graphify export falkordb' path advertised
'redis-cli -x GRAPH.QUERY graphify < cypher.txt', but FalkorDB rejects that
with 'query with more than one statement is not supported' - cypher.txt is a
multi-statement Neo4j script. The individual statements ARE valid OpenCypher
(verified by loading them one at a time), only bulk script import is unsupported.
Message + skill docs now say so and point to --push (the verified load path).
Makes the FalkorDB option a first-class sibling of Neo4j in the agent skill,
not just the export CLI:
- --falkordb / --falkordb-push shorthands documented in core.md + the shared
exports.md reference, so they render into all modular platform skills and
read exactly like --neo4j / --neo4j-push. (The aider/devin monoliths are
diff-frozen vs v8 by skillgen's roundtrip guard, so they are left untouched.)
- README command reference switched to the /graphify ./raw --falkordb-push form.
- Documented URI scheme is now falkordb://localhost:6379; the scheme is only
informational (host/port are parsed out), so redis:// or a bare host:port
remain equivalent. Regenerated skill artifacts + expected/ snapshots.
The Agent Skills spec only defines name, description, license,
compatibility, metadata, and allowed-tools as valid frontmatter fields.
The trigger: /graphify line was non-spec, silently ignored by spec-
following hosts, and flagged by agentskills validate CI checks.
- gen.py: removed trigger emission from _render_frontmatter; added
_is_trigger_line() helper for roundtrip allow-list
- fragments/core/aider.md: removed hardcoded trigger: /graphify
- platforms.toml: removed trigger doc comment and trigger="" entries
- test_skillgen.py: replaced trigger-assertion tests with a single
test asserting no host has trigger: in frontmatter
- Regenerated all 125 skill artifacts
Routing intent is preserved: the description field already contains
"treated as a graphify query first" and "graphify-out/ exists".
Co-Authored-By: Claude Sonnet 4.6 <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>
#1174: affected.py load_graph now forces directed=True before
node_link_graph, matching the identical fix in serve.py and __main__.py.
Undirected graphs (directed:false in graph.json) were causing in_edges
to fall back to a direction-blind scan, missing true callers and
reporting false positives. Regression test added.
#1173: post-commit and post-checkout hook bodies now read
graphify-out/.graphify_root before calling _rebuild_code, falling back
to Path('.') if absent. A scoped build (graphify src/) no longer gets
silently expanded to the full repo on the next commit. Tests added.
#1172: Step 9 cleanup split into rm -f for fixed files and
find -maxdepth 1 -delete for the chunk glob. Under fish/zsh an
unmatched glob aborts the entire rm -f line, leaving temp files on disk.
Fixed in the three skillgen source fragments and regenerated.
#1163: detect_incremental type guard on stored mtime — if the manifest
contains a dict-valued mtime (schema drift from older versions), coerce
to None rather than propagating a non-numeric into comparisons.
Regression test added.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
gen.py imported tomllib unconditionally, but that is 3.11+ stdlib only and
graphify supports (and CI tests) 3.10 - so importing tools.skillgen.gen, and
thus collecting test_skillgen.py, crashed the 3.10 test job with
ModuleNotFoundError. Fall back to the tomli backport on <3.11 and add tomli to
the dev group under that marker. Verified the fallback loads and parses with
tomllib forced absent.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
R1: the 6 always-on blocks were read into module-level constants at import,
so a missing/corrupt always_on/*.md crashed `import graphify.__main__` and
bricked every CLI command, not just install. Make _always_on lazy + lru_cached,
raising a clear "reinstall" error only on the install path that needs the block;
a module __getattr__ keeps the legacy constant names importable for the tests.
Verified: deleting a block no longer crashes `graphify --version`.
skillgen baselines: the self-check guards pinned to the moving `origin/v8` ref,
which stops pointing at the pre-split state once the split lands on v8 (the
always-on-roundtrip guard then fails in CI and monolith-roundtrip goes vacuous).
Pin _v8_baseline_ref, ALWAYS_ON_BASELINE_REF, and the two monolith roundtrip_refs
to the immutable pre-split commit SHA, matching the stated "does not track HEAD"
intent; update the 4 tests that asserted the old ref string.
R2: add tests/test_wheel_packaging.py - build the wheel and assert every
references bundle and always-on block ships in it, so a package-data glob miss
can't pass the repo-tree guards yet hard-exit `graphify install` for real users.
Co-Authored-By: Claude Opus 4.8 <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.
Mahaboob pasha