sync from remote upstream#3
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…or, memory hint, and timeout
…hem for algorithmic queries
…val and shell allowlist
…eping diffs visible
…ove DocumentAnalyzer
…dy on count_tokens failure
… pending approvals)
…solution fix(java): resolve field-access chains as method receivers and nested field access
feat(evals): add L2 module-call attribution metric with ast oracle
chore(deps): bump the uv group across 1 directory with 12 updates
… alias decorators
feat(parser): emit module-load CALLS edges for bare decorators
…st modules when tests excluded
…ot a git repo (#542) * feat(cli): validate --repo-path exists, is a directory, and warn if not a git repo * fix(cli): treat .git file (worktree/submodule) as a git repo to avoid false warning
feat(dead-code): treat module-load callees as reachability roots
…RITS reachability
…#543) * feat(cli): add --output-format json to wrap single-query agent output * fix(cli): reject --output-format json without --ask-agent and preserve non-ascii
…RITS reachability (#544) feat(dead-code): report unreachable classes via INSTANTIATES and INHERITS reachability
…ontributing guide
* feat(evals): add graph-vs-grep retrieval benchmark * fix(evals): read ripgrep patterns from stdin and split on NUL for large symbol sets and colon paths
…aced Adds nine independent-oracle eval dimensions to the evals harness and fixes the four cgr bugs they surfaced: incremental cross-file edge drops (#532), method-nested call attribution, Go receiver-method caller qn plus receiver dispatch, and externally-imported-name constructor misresolution.
…ugs it surfaced (#548)
…a call-resolution bugs (#549) * feat(evals): add Java multi-language retrieval eval and fix three Java call-resolution bugs * fix(java): do not resolve unimported bare class receiver to another package
… TS call-graph bugs (#550)
…lls (#551) * fix(js-ts): model class-field arrow members and resolve their body calls * refactor(js-ts): use safe_decode_text and a single value check for arrow binding names
…function-call resolution (#552) * feat(evals): add PHP multi-language retrieval eval and fix plain PHP function-call resolution * fix(evals): drop dynamic PHP member offsets from the call oracle
…s in Lua function-expression bodies (#553)
#545) * perf(query): reuse Memgraph connection in semantic search tools (#505) * Address PR review: QueryProtocol, defensive parsing, async thread offload Use QueryProtocol for ingestor typing to match main.py and other tools. Parse graph result fields with .get() fallbacks. Offload ingestor I/O via asyncio.to_thread in async tool wrappers, matching query_code_graph pattern.
…staining libclang oracle (#554) * feat(evals): add C multi-language retrieval eval graded against an abstaining libclang oracle * docs(evals): correct C retrieval write-up to report the tree-sitter ERROR-region coverage gap * docs(evals): link issue #555 tracking the tree-sitter-c block-comment-in-macro bug * fix(evals): exclude ignored directories from C oracle header include paths
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sync from remote upstream