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MCP server: silent wrong matches on ambiguous/near-miss names, noisy query_graph, misleading list_prs error

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Active
Tech stack
php, python, symfony
Domain
backend-api-design, devtools

Research direction

Start by reproducing the listed calls against the explicit graph.json, then trace the MCP tool entry points get_node, query_graph, get_community, list_prs, get_pr_impact, and get_neighbors. Done means ambiguous and non-exact labels are explicit, graph results are relevance-aware, communities are labelled, repository errors explain repo=, and neighbor truncation preserves incoming edges.

Written by the indexing model from the issue text.

Description

Version: graphifyy 0.9.71 (installed via uv tool), graphify-mcp over stdio, started with an explicit graph.json path.
Codebase: PHP / Symfony bundle, ~11k nodes / ~33k edges, 614 communities.

1. get_node silently picks one match for an ambiguous name

  • Steps: get_node(label="edit") on a graph where several classes define edit().
  • Actual: returns a single node (Controller/VisitController.php L427) with no hint that other candidates exist.
  • Expected: a list of the candidates (path + line), or an explicit "ambiguous, N matches" error. The caller can't tell whether the answer is the right edit().

2. get_node silently resolves a non-existent name to a different node

  • Steps: get_node(label="MailController") when no MailController exists in the codebase.
  • Actual: returns EmailController as if it were an exact match.
  • Expected: "no exact match", optionally followed by fuzzy suggestions clearly labelled as such.

Side note: the path::symbol form works (Controller/VisitController.php::edit → found). get_node(node_id=...) does not find a generated-looking id for a non-existent symbol, which is correct.

3. query_graph is dominated by god nodes

  • Steps: query_graph(question="who sends the convocation emails?"), default depth 3.
  • Actual: BFS starts from 5 seeds and reaches 2,708 nodes. The output is TRUNCATED and mostly made of the highest-degree nodes (framework interfaces, core entities, enums). With token_budget=8000 it is still truncated (240 of 2,708). With context_filter=['call'] only 20 nodes remain, all unrelated test helpers.
  • Expected: rank results by relevance or distance to the seeds rather than degree, or damp hubs during traversal (similar to exclude_hubs_percentile in god_nodes).

4. get_community returns no community label

get_community(3) returns "Community 3 (205 nodes)" with no name or summary. A generated label (e.g. dominant class or directory) would make the output usable.

5. list_prs reports "gh CLI not found" when the real issue is repo detection

  • Steps: list_prs() with no repo argument, the server started on a graph.json outside any git repo.
  • Actual: Error: gh CLI not found or not authenticated. Run: gh auth login. gh is installed and authenticated. Passing repo=owner/name makes it work. get_pr_impact with the same repo works too.
  • Expected: an error such as "could not detect repository; pass repo=".

6. Minor: get_neighbors truncation hides incoming edges

With the default budget, outgoing edges are listed first, so all incoming edges (callers) are cut off on high-degree nodes. Listing incoming edges first, or balancing both directions, would help.

Dominant language
Python
Stars
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Forks
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