Node ID collisions when multiple files share the same stem (e.g. Program.cs)

[V0v1kkk]

Problem

_make_id(stem, name) uses only the file stem to generate node IDs. When a project has multiple files with the same name in different directories (e.g. src/App1/Program.cs and src/App2/Program.cs), their nodes collide — methods from both files merge into a single node, producing an incorrect graph.

This is common in .NET solutions where each project has its own Program.cs, Startup.cs, AssemblyInfo.cs, etc.

Proposed Fix

Add a post-extraction pass that detects colliding node IDs (multiple nodes from different source_file paths sharing the same ID) and disambiguates them by prepending the parent directory name.

For example:

• program_program → app1_program_program and app2_program_program

Impact

Tested on a .NET solution with 2 Program.cs files — nodes are now correctly separated.

I have a PR ready.

[GustavoStingelin]

same problem here, this is very common in golang side tho

[maticijus]

Confirming this issue is language-agnostic — Python repro on graphifyy v0.5.0:

A trading-system codebase has 14 separate cli.py files, one per skill (insider-flow/cli.py, npt-delta/cli.py, sector-flow/cli.py, x-cashtag/cli.py, data-store/cli.py, signal-enrichment/cli.py, risk-manager/cli.py, confirmation-signals/cli.py, …).

All 14 main() functions collapse to a single node ID cli_main (format {stem}_{symbol}). Result:

• That phantom node ranks Wroked out examples missing graph.html #3 god node, degree=115
• 85 of 115 neighbors land in one community (because that's where the collision-edges glue everything to)
• 30 cross-community edges spread across 11 communities — looks like a major architectural bridge but is actually 14 independent CLI scripts each touching their own local helpers

Same root cause as the Program.cs case in this issue. Worth noting the fix should cover the entire common-filename family in idiomatic Python:

cli.py, __init__.py, __main__.py, types.py, utils.py, helpers.py, conftest.py, tests.py, models.py, schemas.py

…and JavaScript:

index.js/.ts, App.jsx, types.ts, utils.ts

Proposed fix in the issue (post-extraction collision-detection pass that disambiguates by source_file) would resolve all of these.

[V0v1kkk]

@maticijus thanks for the detailed Python repro — 14 cli.py files collapsing into a single god node is a great example of this issue in the wild.

The fix in PR #441 handles all of these cases. It detects colliding IDs (from any language — C#, Python, JS, Go, etc.) and disambiguates them using progressively deeper path components from the source file. So insider-flow/cli.py → insider_flow_cli_main, npt-delta/cli.py → npt_delta_cli_main, etc.

Latest push also fixes an edge case where the renamed ID could shadow an existing node from a different group (reported by @Qodo-Free-For-OSS on the PR).