AST extractor produces ID collisions on identical filenames across folders, merging distinct functions into one node #952

Bug

graphify.extract (AST mode) generates node IDs from {filename_stem}_{symbol}. In monorepos where many folders contain a same-named file (e.g. Next.js App Router with one action-bar/index.tsx per feature, or one lib/atom.ts per feature), every function with the same name across those files collapses into a single graph node. The union of their edges then creates phantom cross-module "bridges" that don't exist in source.

Repro

In a Next.js repo with structure:

app/(innerPages)/<feature>/action-bar/index.tsx   # each exports `function ActionBar()`
app/(innerPages)/<feature>/lib/atom.ts            # each exports `useFeatureAtom`

Run graphify . on a code-only corpus.

Result: a single node action_bar_index_actionbar accumulates contains edges from ~16 distinct files and calls edges to atoms from ~10 unrelated features. god_nodes() reports it as the most connected abstraction. surprising_connections() flags fake cross-feature bridges.

Expected

IDs should be unique per source file, e.g. derived from the full relative path (innerpages_<feature>_action_bar_index_actionbar) or filepath hash, so functions with identical names in different folders remain distinct nodes.

Evidence

In one 552-file scan, 16 action-bar/index.tsx files merged into 1 node showing 30 edges and 0.167 betweenness — entirely an artifact.

Suggested fix

Change ID generation in the AST extractor to use the relative source path (slashes → underscores) instead of just Path(...).stem. This is also what the Step 3 prompt instructs semantic subagents to do, so the AST extractor would just be matching its sibling.

Version

graphifyy from PyPI, Python 3.x via pipx.