A table no file defines, read from N files, becomes N per-file stub
nodes, and a schema-qualified read never binds to its definition in
another file. A SQL read of `Orders` also binds to a Python class
Orders. Guards cover same-file binding and different schemas.
(cherry picked from commit 1dfc710497)
A GO line with no `;` before it is read as an identifier, so the next
statement lands in an ERROR node and its table is lost. Guards cover
`;`-terminated batches, GO inside a block comment, a column named go,
and GO after a keyword line such as SET NOCOUNT ON.
(cherry picked from commit f00ecc42c9)
tree-sitter-sql has no T-SQL bracket identifiers and no create_procedure
node, so bracket names were mangled and procedures only got a node from
the regex recovery, never an edge. Labels and lookup keys now drop the
brackets (ids are unchanged). Each recovered routine's body, up to the
next CREATE/ALTER, a GO line or EOF, is scanned on the masked text:
FROM/JOIN give reads_from, and INSERT/UPDATE/DELETE/MERGE/SELECT INTO
give writes_to. Alias updates resolve to their table; CTEs, variables
and temp tables are skipped.
AST cache schema 20 -> 21 so cached .sql extractions re-run.
(cherry picked from commit 70f521dba9)
Bracket names like [dbo].[Orders] come out as the label `dbo].[Orders`,
stored procedures get no reads_from edges in any dialect, and
INSERT/UPDATE/DELETE/MERGE make no edge. Guards cover aliases, CTEs,
temp tables, variables, comments, strings and body boundaries.
(cherry picked from commit a2a666c6d7)
`get_node` / `get_neighbors` share `_resolve_single_node`, which takes the
first node of the winning tier. The substring tier matches a query anywhere
inside a label, so `get_node(label="MailController")` on a codebase with no
`MailController` returned `EmailController` as if it were the exact symbol,
with no hint that the name does not exist.
The resolver now splits the two fuzzy tiers by intent. A prefix match still
resolves, because the caller started typing the real name (`email` ->
`EmailController`). A substring-only match is a search hit, not the symbol
the caller named, so it returns `No exact match for '<query>'` followed by
up to five closest names with their source location, plus a `path::symbol`
retry example. `get_neighbors` inherits the same answer through the shared
resolver, so both tools report one lookup the same way (ADR-0001).
Exact, source-exact and prefix resolution, the ambiguity refusals, the
dotted/Python and `path::symbol` forms and scoring are unchanged. The other
near-miss case in the issue (`get_node(label="edit")` with several `.edit()`
methods) already refused as Ambiguous under ADR-0001; tests cover both.
Tests: the issue's MailController repro, prefix shorthand, exact-over-substring
precedence, the five-candidate cap.
(cherry picked from commit d3875f4f1c)
A cross-repo `calls` edge took its `source_file` from the caller node
(an ObjC method node is minted at its `@interface` in the `.h`) while its
`source_location` is the call-site line, recorded in the `.m`. Pairing the
two pointed `source_file:source_location` into the wrong file — often past
the end of a short header.
The park payload now carries the call-site file alongside the line, and
`link_cross_repo_member_calls` prefers it, falling back to the caller
node's file for pre-#3152 graphs. The parked path is relativized in the
same extract-time pass that relativizes node source_files, so it never
leaks the absolute checkout path into graph.json.
Co-Authored-By: Claude Code <noreply@anthropic.com>
(cherry picked from commit 3281d42492)
The #2543 heal re-queues any manifest-stamped code file that has a
registered extractor but zero nodes in graph.json, treating it as a
poisoned stamp. A file the extractor declines by design (data JSON such
as .xcassets Contents.json, #1224/#2879) is exactly that shape — stamped,
zero nodes — yet legitimate, so the heal re-queued it on every incremental
run forever.
extract() now surfaces the declined files (skipped_sources), save_manifest
marks their row ast_empty: true (preserved across unchanged incrementals,
dropped once a file starts producing nodes), and the heal skips rows
carrying the marker. A pre-fix manifest has no marker, so such a file is
re-queued exactly once, re-stamped with the marker, and left alone after.
Co-Authored-By: Claude Code <noreply@anthropic.com>
(cherry picked from commit c930591f08)
`_merge_decl_def_classes` folds an @interface/@implementation pair into one node
only when both live in the SAME directory (the id embeds the directory path,
#1556). A class whose `.h` sits in `include/` and `.m` in `src/` therefore mints
two same-labelled nodes that never merge, so `[w render]` saw two type-def
candidates, tripped the member-call resolver's single-definition god-node guard
(`if len(type_defs) != 1: continue`), and emitted NO edge -- the same corpus
resolved fine when the pair shared a directory. Header/impl directory splits are
common layout, so this hit ordinary code.
Replace the three per-arm god-node bails with a shared `_resolve_member_target`
that unions the candidates' members and binds the selector to the sole candidate
that DEFINES it (an @implementation in `.m`/`.mm`, or a merged node carrying
`definition_file`). A header-only node is a bare declaration and does not count,
so the split pair resolves to its one real definition. Two unrelated same-named
classes that each define the selector still yield two definitions and stay
ambiguous -- the guard holds for the genuinely-ambiguous case it was meant for.
Co-Authored-By: Claude Code <noreply@anthropic.com>
(cherry picked from commit 510934c686)
The review bot flagged a real hazard in the owner-evidence bookkeeping: a
mention whose `references` edge is already in the graph returned early, so
the document never recorded that it cites the target. A later bare method
mention in the same document then lost its owner and was dropped.
`_add` now records the cited target before it decides whether the edge has
to be written, so the evidence survives an edge that is already there.
The pipeline cannot reach that state today (the resolver is handed a fresh
edge list, and the incremental context only carries contains/method/
inherits/imports edges), so this is hardening rather than a fix for a
reachable failure. The regression test drives the resolver directly with a
pre-existing class edge.
(cherry picked from commit 37efe877cf)
`resolve_markdown_mentions` linked any bare, parenthesis-less code span to
the corpus's single `_callable` carrying that label, and methods qualify.
A prose word in a code span (`redis` the server, `data`, `message`) then
became `heading --references--> SomeClass.word()` at INFERRED 0.95, on a
method that has nothing to do with the sentence. On the reporter's corpus
44 of 1,906 mention edges were words of this kind.
A bare single-name span is now resolved in three passes. Explicit evidence
(a cited path, a dotted qualifier chain, or a trailing `()`) resolves as
before. Bare mentions that do not name a method keep resolving, and their
targets are recorded per document. A bare mention that names a method is
kept only when its owner class is already cited in the same document, so
`redis` no longer links to `Cache.redis` while `successWithWarnings` next
to `HandlerResult` still does. Ambiguity, built-ins and the case-sensitive
label match are unchanged.
Tests cover the issue repro, the owner-cited case, the `()` case, a free
function, and the cross-document guard.
(cherry picked from commit 6bba91fc65)
#4655 added amp/copilot/kilo/kimi to the hand-maintained --help install
line but still omitted antigravity-windows, so it disagreed with
_print_install_usage. Derive the list from the same
[*_PLATFORM_CONFIG, "gemini", "cursor"] expression the install usage
uses so the two cannot drift, and add test_help_lists_every_install_platform
to catch any future platform that is not advertised.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
An ObjC category (`@interface Foo (Cat)` in `Foo+Cat.h`) keys its class
node and methods off the base stem `Foo`, so they fold into `Foo.h`'s
class (#1556). extract() turns an id minted from an absolute input path
into the repo-relative form only when it starts with its own file's stem
prefix (`.../Foo+Cat`), so these ids kept the absolute form. A category
on a class outside the corpus (`NSString (Extra)`) got a node id with
the checkout path in it, and so did the methods of a category on an
in-corpus class. graph.json then carried the path (#502), two checkouts
of one repo gave different graphs, and an incremental rebuild in a moved
or copied checkout added duplicate nodes.
The remap now also registers a category file's base-stem prefix, after
the file's own prefixes. On SDWebImage, AFNetworking and Kingfisher,
334 / 51 / 17 ids carried the checkout path; now 0, two checkouts give
identical graphs, and absolute and relative input agree. Every edge,
compared by label and file, is unchanged. Through the CLI, SDWebImage's
graph drops 125 duplicate category nodes (a leaked copy beside the clean
copy reached through its include/ symlink) and one false reference.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
(cherry picked from commit 11fe66a3cf)
`--transport http --host ::1` put the bare literal into the DNS-rebinding
allowlist (`::1`, `::1:8080`), but clients reaching http://[::1]:8080
send `Host: [::1]:8080`, so every request was rejected with 421 and the
server was unusable on an IPv6 loopback bind. Bracket an IPv6 literal
before building the allowlist; foreign Host headers are still rejected.
(cherry picked from commit 831b25703c)
Binary captures pick their filename with lstat so they never replace an
existing directory entry (#4393). Text captures (webpages, tweets, arXiv)
still used Path.exists(), which follows symlinks: a dangling symlink named
like the capture reported "free" and write_text() followed it out of the
corpus directory. The loop also stopped at 999 numbered names and then
overwrote the last one. Share the lstat-based selection between both
paths.
(cherry picked from commit 3e483ca077)
The claude and gemini hooks (since #522/#1987) double-quote a resolved graphify path containing spaces, but _install_codex_hook embedded the resolver output raw. On a checkout path like 'D:/Project V2/.venv/Scripts/graphify.EXE', every shell that runs the hook (Git Bash on Windows to cmd.exe to POSIX sh) word-splits the command at the first space: the guard can never fire, and #2165's subcommand-parsing test splits at the same space and fails.
Mirror _claude_pretooluse_hooks/_gemini_hook with the same two-line guard: bare-name (project-scoped, #3129) installs are unaffected, as is any absolute path without spaces. test_codex_hook_command_is_a_real_cli_subcommand now parses hook commands with shlex.split instead of naive .split(), and a new regression test installs all three hosts under a spaced resolver output, proves argv[0] survives intact, and re-verifies uninstall recognition of the quoted entry.
(cherry picked from commit 87e997d3a0)
A \const X = require('./m')\ binding is an import, not a module-scope data
binding. The node it produced in the importing file shadowed the class the
required file exports, so \
ew X()\ bound to the local node and the
required class got no incoming edge.
(cherry picked from commit 66bb69114a)
Covers the issue's own repro, a delegating wrapper that no longer
self loops and an unrelated same named sibling that no longer steals
the edge, plus three controls: a bare unqualified call still
resolves by name, this dot calls still bind through the caller's own
class, and a TypeScript typed receiver still resolves through its
declared type. A fourth control checks that a factory object's own
sibling methods still call each other, the one legitimate case that
keeps resolving locally instead of deferring.
(cherry picked from commit 49c645d2ff)
_parse_pom collected every <dependency> in the file with
".//dependencies/dependency", including <dependencyManagement> entries,
which only pin versions, and the <dependencies> of build plugins. Each
became a depends_on edge, so a parent POM that manages its modules'
versions depended on every module.
Read <dependencies> under <project> and under <profiles><profile>, where
Maven takes a project's dependencies from.
(cherry picked from commit 534177d1ea)
The partial-read coverage check (#3987) adds a python block between the
Step B3 merge and Part C. Two skill-path tests that landed separately in
the 0.9.9x skill work hard-code the block count in that range (3) and
then execute every block in it. Bump the expected count to 4; the
behavioral assertions (token sums, merged node sets, stale-chunk
clearing) still hold because B3.5 only writes an empty
.graphify_partial.txt on the all-cached and codex-merge paths.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The Read tool returns at most 2000 lines per call and reports no error when it
truncates, so a subagent that read only the head of a long file still writes a
well-formed chunk. Step B3 treated "chunk exists and parses" as success, and
because build_merge replaces a re-extracted file's nodes, the unread tail was
not merely missed: it was deleted, the run reported success, and the manifest
recorded the file as done so no later --update retried it. On a 4165-line file
that left 103 nodes covering 31% of the document, with 90 of 131 entries gone
and the manifest treating it as finished.
Three changes, in the fragments, so all thirteen disk-dispatching hosts pick
them up from one edit:
The extraction spec (verbose and compact) now states the cap and forbids
emitting nodes for a partly-read file, and asks the subagent to report a
top-level "coverage" map of file -> lines read. A short count is recoverable; a
missing entry is indistinguishable from a complete read, which is why the
machine check needs the prompt to ask.
Step B1 bounds a chunk by total lines as well as file count (20-25 files AND
~6000 lines), and gives any file past 2000 lines a chunk to itself. File count
alone was only half the mechanism: a subagent holding 25 files also dilutes
attention, which is how a 590-line plan came back with zero nodes.
Step B3.5 compares each reported coverage against the file's real length, names
what was short, and hands the list to the two places that decide whether a file
is ever looked at again: save_semantic_cache(partial_source_files=...) stamps
those entries partial, which load_cached treats as a miss, and
_stamped_manifest_files(partial_source_files=...) leaves them unstamped so
detect_incremental re-queues them. Both are the existing contract the library
path already uses for a truncated LLM response (#933, #1950), so the skill and
library paths now recover the same way. Nodes already found for those files are
kept; the next run's replace-on-re-extract swaps them for a complete set.
The check is fail-safe in the direction that loses nothing: no coverage reported
means no file is flagged, and a flagged file is re-read rather than trusted.
Codex collects subagent results in memory with no per-chunk files on disk, so it
gets the prompt-layer fix but not the Step B3.5 gate; its inline extraction has
no chunk file to compare against.
Tests execute the emitted python instead of matching its source (the #2126/#2641
convention), including a round trip through the real semantic cache: the
partly-read file must come back as uncached, while the fully-read file still
hits. Reverting the fix makes that round trip return an empty uncached list -
the file served from cache forever, which is the bug.
Fixes#2225
(cherry picked from commit 0b6a1868af)
The ambiguous-name refusal added in #4517 routed through _resolve_single_node,
whose winning tier can be a prefix or substring match, so a bare search keyword
that merely substring-matched several labels was wrongly refused: `query "client"`
returned EXIT 3 because it is a substring of `AlphaClient`/`BetaClient`. That
narrowed query's keyword-search semantics.
Adds _query_name_refusal, which refuses only when the term EXACTLY names several
nodes (the source_exact/exact tiers) -- #4511's `.nonce()` case -- and otherwise
falls through to scoring. The `query` and `--seed` paths use it; explain/path/
get_node keep _resolve_single_node, whose prefix/substring tiers are correct for a
direct node lookup. Adds a regression test that a substring keyword still searches.
Co-Authored-By: shivampal46011 <shivampal46011@users.noreply.github.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
query guessed a node when the same name existed in several files, and an ambiguous --seed still exited 0. explain and path already refuse that lookup. query now returns the same candidate list and exits 3, and a --seed that matches nothing exits 4.
_shebang_interpreter returned the interpreter exactly as written, and both
detect's _SHEBANG_CODE_INTERPRETERS and extract's _SHEBANG_DISPATCH list
only the generic names. An extensionless CLI starting with
#!/usr/bin/env python3.12, #!/usr/bin/python2.7 or #!/usr/bin/lua5.4 was
classified as None and silently left out of the scan. Map a version
suffix on a known interpreter back to that interpreter (python3.12 ->
python3, lua5.4 -> lua) in the shared parser, so detection and extractor
dispatch both see it. Unknown names are left as they are.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
extract_pdf_text wrapped the whole PdfReader loop in except Exception:
return "", so a malformed or encrypted PDF looked exactly like a PDF with
no text and dropped out of the graph with no trace. Keep returning ""
(callers rely on it), but print a warning naming the file and the error
first. Warn once per path, since detect() and the semantic pass both read
the same file.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Obsidian writes wikilink paths from the vault root, so scanning a folder
below it meets links like [[Corp/wiki/Fox]] from inside Corp/. The
vault-wide fallback matched them as suffixes of root-relative paths,
which never succeeds, and the references edge was dropped. When nothing
matches, drop the longest leading run of the scan root's own folders
and match the rest exactly from the root.
_run_cli refreshed stale skills and old OpenCode plugins before the
--version/--help early returns, so checking what was installed rewrote
SKILL.md, left a .bak and restamped .graphify_version. Skip both
refreshes for version, help and `<cmd> --help`; the stale-skill warning
still runs, since it only reads. Free-text commands keep refreshing.
Carries the tests that belong with the module-call exact-name fix (#4577): the
fix landed via the PR's follow-up perf commit, which did not include the test
file. Adds the PR author's five cases (exact-name function/class resolution,
aliased import, fold-only fail-closed) plus a negative cross-module case proving a
call never binds to a same-named child of an UNRELATED module -- the one headline
risk of re-bucketing by exact name.
Co-Authored-By: madhusudanpatnaik <madhusudanpatnaik@users.noreply.github.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Follow-up to #4566. Adds an opaque (non-JWT) `Bearer <token>` shape to the
credential redactor so `Authorization: Bearer <opaque>` is redacted (the JWT form
was already caught by the eyJ pattern); the word "Bearer" is kept, only the token
is replaced. Adds an over-redaction regression test proving a 40-char git SHA, a
sha256 digest and a UUID pass through untouched, so the redactor never mangles the
ordinary high-entropy identifiers that appear in real rationale labels.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Metal (.metal) and CUDA (.cu/.cuh) are C++-derived GPU languages that route
through the C++ extractor, but their qualifiers are not part of the C++ grammar:
- Metal address-space / function qualifiers: `device`, `constant`,
`threadgroup`, `thread`, `kernel`, `vertex`, `fragment`, ...
- CUDA execution-space / memory qualifiers: `__global__`, `__device__`,
`__host__`, `__shared__`, `__constant__`, `__forceinline__`, ...
tree-sitter-cpp parses a leading qualifier as the declaration's
`type_identifier` (the real type is pushed into an ERROR node), and
`_cpp_collect_type_refs` emitted it as a type reference. Each qualifier then
became a sourceless, corpus-shared god node that every shader/kernel
`references` (e.g. `kernel`/`device`/`constant` on sample.metal,
`__global__`/`__device__`/`__host__` on sample.cu, the CUDA ones colliding on
ids `global`/`device`/`host`). That is a provenance violation — a node with no
source_file — and the hubs also pollute god-node rankings in analyze.
Skip a fixed per-extension set of dialect qualifier keywords in the C++
type-ref collector, keyed by file extension so plain `.cpp`/`.cc`/`.h` files
are untouched (there these words are legal identifiers and still resolve as
real user types). Genuine user types in the shader/kernel (the `Vec3` struct)
are preserved.
Documented limitation: `constant Foo* p` buries the real `Foo` type inside the
ERROR node, so `Foo` is not recovered; this change only removes the bogus
qualifier node.
Docstrings and `# WHY:`/`# NOTE:` comments become rationale node labels,
which are persisted verbatim to graph.json, graph.html, GRAPH_REPORT.md and
the AST cache. A token pasted into a comment therefore ended up in the
artifacts the README tells users to commit and share.
Add security.redact_secrets() (shape-based: vendor-prefixed tokens, PEM
private-key headers, JWTs, URL passwords) and apply it in
_shorten_rationale_label(), before truncation so a cut can't leave a partial
token. That helper is shared by the Python and JS/TS rationale extractors.
Related to #2781 (document text sent to LLM backends unredacted); this
covers only the comment/docstring -> graph path.
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
A C-API header guarded by `#ifdef __cplusplus extern "C" {` has no
class/namespace/template/:: marker, so `_is_cpp_header` left it on
extract_c. The C grammar rejects the linkage block and the header
extracts zero symbols (e.g. whisper.cpp's include/whisper.h and
include/parakeet.h), dropping the project's public API from the graph.
Add `extern "C"` to `_CPP_HEADER_MARKERS`. ObjC sniffing keeps priority.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Since #4500, graph.json carries "multigraph": true whenever it holds
parallel edges (imports and calls between the same pair, say), and
graphify export loads it as a MultiGraph. to_graphml's attribute
coercion indexed edges as H.edges[u, v], which needs a key on a
MultiGraph, so graphify export graphml crashed with "not enough values to
unpack" and wrote nothing. Iterate edges(data=True) instead, which works
for both graph types and keeps every parallel edge.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
gh's statusCheckRollup mixes CheckRun entries (status/conclusion) with
StatusContext entries, the commit statuses external CI such as Jenkins or
CircleCI posts, which carry only a state. _parse_ci never read state, so a
failing external CI showed as NONE, or as SUCCESS beside a passing check
run, and the PR was classified READY instead of CI-FAIL in pr list,
triage and the MCP PR tools. Fold state into the conclusions, with ERROR
as a failure and PENDING/EXPECTED as pending.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The git symbolic-ref fallback in _detect_default_branch kept only the last
path segment of refs/remotes/origin/<branch>, so a default branch named
release/2.x came back as 2.x and every PR targeting it was classified
WRONG-BASE. Strip the refs/remotes/origin/ prefix instead.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Swift 5.9 macros were dropped entirely. `macro stringify(...) = #externalMacro(...)`
parses as a `macro_declaration` (freestanding or attached), which was in neither
`function_types` nor `class_types`, so the symbol never entered the graph. A
freestanding call `#stringify(...)` parses as a `macro_invocation`, not a
`call_expression`, so its call edge was lost too.
- Add `macro_declaration` to the Swift `function_types`. It has no `name` field,
but the name is a bare `simple_identifier` child already covered by
`name_fallback_child_types`, so the existing name resolution handles it; the
generic `<T>` type parameter is excluded by the existing type-param scope pass
(no `t` god node).
- Add `macro_invocation` to `call_types` and give it a callee branch in
walk_calls: a freestanding macro is a free top-level symbol (resolved by bare
name, no `self` receiver). Calls inside the macro's arguments
(`#stringify(helper())`) still resolve because walk_calls recurses into the
invocation's children.
Attached-macro *usage* (`@AddCompletion` on a type) is an attribute, not a
`macro_invocation`, so it is not linked to the macro — left unresolved
(fail-closed); the declaration itself is still extracted.
A C# `delegate` is a named type, but `delegate_declaration` was in neither
`class_types` nor `function_types`, so the declaration was dropped from the
graph. A field or parameter typed as the delegate (`public BinOp Op;`,
`int Apply(BinOp f, ...)`) still resolved the name `BinOp` through
`ensure_named_node`, which minted a *sourceless* stub and pointed the
`references` edge at it — even though `BinOp` is declared in the same file.
That violates the provenance invariant: a real source-backed declaration must
not lose to a sourceless god node (and the bare-id stub becomes a cross-file
hub shared by every same-named reference in the corpus).
`delegate_declaration` has a `name` field and no body, so adding it to the C#
`class_types` emits a clean empty type node (no phantom members) that the
in-file references now bind to. Namespaced delegates are scoped and contained
exactly like the sibling class/enum/struct declarations.
Delegate parameter/return type references and delegate-instance invocation
resolution are unchanged (out of scope).
A Kotlin `typealias` is a named type, but `type_alias` was in neither
`class_types` nor `function_types`, so the declaration was dropped from the
graph. A property or parameter typed as the alias (`var onClick: ClickHandler?`,
`fun handler(h: ClickHandler)`) still resolved the name `ClickHandler` through
`ensure_named_node`, which minted a *sourceless* stub and pointed the
`references` edge at it — even though the alias is declared in the same file.
That violates the provenance invariant: a real source-backed declaration must
not lose to a sourceless god node (and a bare-id stub becomes a cross-file hub
shared by every same-named reference in the corpus). Scala and TypeScript
already model type aliases as nodes, so Kotlin was the inconsistent outlier.
`type_alias` has an `identifier` name (covered by `name_fallback_child_types`)
and no body, so adding it to the Kotlin `class_types` emits a clean empty type
node (no phantom members) that the in-file references now bind to.
_fold_confidence normalized the confidence/confidence_score pair on edges
and hyperedges, but nodes passed through the build verbatim, so a model
emitting a lowercase enum value, a bare float, or a drifted word for a
node's confidence landed in graph.json as-is. Fold it in
_fold_node_aliases, which both build_from_json and build_merge already
call, so nodes share one normalization contract with edges.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
When a labeling reply is cut off mid-object, _parse_label_response falls
back to a regex that pulls the complete "<cid>": "<name>" pairs, but it
used the captured string body as-is. Escapes such as \u00e9 and \" then
ended up in the community name as literal backslashes, while the same
name in a complete reply decoded correctly. Decode each salvaged value as
a JSON string body, keeping it unchanged when it is not a valid one.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Windows PowerShell 5.1 (Set-Content -Encoding UTF8) and older Notepad save
UTF-8 with a BOM. load_graphifyrc read the file as plain utf-8, so the BOM
became part of the first key; unknown keys are ignored by design, so that
setting (say language.inc=php) vanished without a warning. Read with
utf-8-sig, as the other Windows-edited files in the repo already are.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The Pi skill rendered the shared agent-tool-disk dispatch, which tells the
host to use subagent_type="general-purpose". pi-subagents has no agent by
that name and rejects it as unknown, so semantic extraction never started
(#4494). Step B3's re-run hints named the same agent.
Pi now gets its own dispatch fragment that sends one builtin `delegate`
agent per chunk; delegate has read, bash, edit and write. The two B3 hints
are core slots filled per dispatch variant, so every other host renders
byte-identical output.
(cherry picked from commit a0b3a053a5)
`extractors/markdown.py` read the scan root of the extraction in flight with a
function-local `import graphify.extract` + `getattr(_extract,
"_XAML_ACTIVE_EXTRACT_ROOT", None)`. That violates MIGRATION.md invariant #4
("never import from graphify.extract inside this package; direction is
extract.py -> extractors/"), and the `getattr(..., None)` meant a rename of the
module global would silently disable Markdown wikilink (Obsidian vault)
resolution rather than fail loudly.
Move the ambient scan root onto `extractors/base.py` — where the extractors
legitimately live — as `set_active_scan_root()` / `active_scan_root()`.
`_safe_extract_with_xaml_root` now publishes the root there (still saving and
restoring for nested extraction), the two XAML readers and the Markdown vault
lookup read it through the accessor, and `markdown.py` imports it in the correct
direction. The `_XAML_ACTIVE_EXTRACT_ROOT` module global in extract.py is gone;
nothing else referenced it.
Behavior is unchanged — the same process-global root is set around each
extraction and read by the same sites. Tests assert the extractor no longer
imports graphify.extract (fails on the old code), that the set/get/restore
contract nests correctly, and that markdown's accessor IS the base accessor.
The markdown, XAML/dotnet, and language suites stay green; the only failures on
this machine are the pre-existing v8 baseline set (c-include determinism,
wikilink-unicode, two watch cwd-deleted cases), which fail identically on clean
v8.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JJbLfztSxm2tH5cJwBbe9q
(cherry picked from commit 86721f765d)
Covers every shape the issue reports: the non numeric drifted words,
a numeric looking string that still backfills confidence_score, a
case only variant that gets recased rather than treated as an
unknown word, the three valid spellings staying untouched, and the
new hyperedge fold. A build_from_json test reproduces the issue's
own warning text end to end and checks it no longer prints.
(cherry picked from commit da369c5ea8)
Covers the exact repro from issue 4492: a node with a source_file and
one without, sharing an id that neither file encodes. Checks both
arrival orders keep the sourced node, matching the sibling order
independent tests already covering the lifecycle and path form
tiebreaks right next to it.
(cherry picked from commit 151becb880)
bash runs the backticked text in Part C's comment when graphify is on PATH, which broke the test in CI. The blocks do not need it. Also narrow three Optional values for pyright. The test checks the same things.
(cherry picked from commit e487672683)
Deepjyoti-Sarmah