[Bug]: inconsistent agent instructions

[SvenMeyer]

Pre-flight checks

• I have checked the Troubleshooting section in the README

What happened?

I initialized with graphify install and this section gets added to AGENTS.md

## graphify

This project has a knowledge graph at graphify-out/ with god nodes, community structure, and cross-file relationships.

When the user types `/graphify`, use the installed graphify skill or instructions before doing anything else.

Rules:
- For codebase questions, first run `graphify query "<question>"` when graphify-out/graph.json exists. Use `graphify path "<A>" "<B>"` for relationships and `graphify explain "<concept>"` for focused concepts. These return a scoped subgraph, usually much smaller than GRAPH_REPORT.md or raw grep output.
- Dirty graphify-out/ files are expected after hooks or incremental updates; dirty graph files are not a reason to skip graphify. Only skip graphify if the task is about stale or incorrect graph output, or the user explicitly says not to use it.
- If graphify-out/wiki/index.md exists, use it for broad navigation instead of raw source browsing.
- Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context.
- After modifying code, run `graphify update .` to keep the graph current (AST-only, no API cost).

on the web app https://app.graphify.com/sum/mcp these instructions are suggested to be copied into AGENTS.md

<!-- graphify-rules-start (managed by `graphify init`) -->
## Use Graphify before grep

This repository is indexed by Graphify: a code graph over its call, dependency, and test structure, exposed through a connected Graphify MCP server. Before reaching for grep or reading files, use the Graphify tools your MCP client lists (their exact names and descriptions are in the server's tool list) for what the graph knows and a text search does not:

- find where a symbol, function, or class is defined (instead of grepping for it)
- understand how something works, or where a behavior is handled
- find who calls a function, or what it calls
- see what a change affects (its blast radius) and which tests cover it
- map a file's dependencies and dependents

Fall back to grep or file reads only for what the graph does not model: literal string or comment matches, non-indexed files, or reading a file you have already located. If no Graphify tools are listed, check the MCP server connection.
<!-- graphify-rules-end -->

Which one has precendence, is the correct or better one ?

Steps to reproduce

see above

Error output or graph output

not tested

Graphify version

0.9.71

Operating System

Linux

Python Version

3.13

Installation Method

uv tool install (recommended)

Additional Environment Details

python version : 3.14.7

Additional context

No response

[github-actions]

Thanks for opening this issue, @SvenMeyer. A maintainer will take a look soon.

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