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[Bug]: graphify tree ignores the repo tag on merged graphs: no per-repo roots, and identical relative paths from different repos collapse together

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Since Oct 17, 2026.

  • #4525 by @AromalBiju1 — open

Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
76/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Active
Tech stack
python
Domain
developer-experience

Research direction

Start in tree_html.py at build_tree, which currently ignores the merged nodes’ repo attribute; then read the tree tests in tests/test_tree_html.py. Reproduce with two repos that share src/engine.py and inspect whether their nodes collapse into one file node. Done when the tree shows separate repo roots and preserves each repo’s directory and file hierarchy, including with --root.

Written by the indexing model from the issue text.

Description

bug
Pre-flight checks
  • I have checked the Troubleshooting section in the README
What happened?

On a graph produced by graphify merge-graphs, graphify tree does not use the repo attribute that merge-graphs sets on every node. As a result:

  1. There are no per-repo roots. The root is the common prefix of the repo-relative source_file values, which is empty when the repos differ, so the viewer title is "/".
  2. Files that share a repo-relative path in different repos (e.g. src/engine.py in both) collapse into ONE file node with all of their symbols interleaved.

Expected: each repo tag is a top-level root with its own directory/file hierarchy built from that repo's relative paths. This would also fix --root on merged graphs, since each repo subtree would be anchored by its tag rather than an absolute path.

Steps to reproduce
1. Create two graph.json files (repo-a, repo-b) whose nodes have source_file "src/engine.py".
2. graphify merge-graphs repo-a/graphify-out/graph.json repo-b/graphify-out/graph.json --out world/graphify-out/graph.json
3. graphify tree --graph world/graphify-out/graph.json --output WORLD_TREE.html
4. Or inspect directly: python3 -c "import json; from graphify.tree_html import build_tree; print(build_tree(json.load(open('world/graphify-out/graph.json'))))"

Merged nodes do carry `repo: "repo-a"` / `"repo-b"` and `local_id`, so the data needed to group by repo is present. tree_html.py never reads `repo`.
Error output or graph output
build_tree output (name, total_count), both repos sharing src/engine.py:

engine.py (8)
  src (8)
    engine.py (8)
      Cls (1) x4
      fn (1) x4

Symbols from repo-a and repo-b are mixed under one file node. Viewer title: "/".
Graphify version

0.9.92

Operating System

Linux

Python Version

3.13

Installation Method

uv tool install (recommended)

Additional Environment Details

No provider environment variables set. Reproduced on a fresh shallow clone of main at the 0.9.92 release commit.Also reproduced with a fresh uv venv; same result.”

Additional context

Suggested fix: in build_tree (tree_html.py), if nodes carry repo, group by it first and build each repo's subtree independently under a root named after the tag. A test in tests/test_tree_html.py with two repos sharing a relative path would cover it.

Related to #4522 (merged-graph tree rendering), but a different cause: here source_file is intact and the repo tag is simply unused by tree.

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