Add codebase navigation to project context skill

[yuecideng]

Description

This PR expands the canonical project development context skill from explicit context reads and maintenance into live codebase navigation.

It:

• adds a navigate mode for locating files, configs, defaults, entry points, registration paths, and recommended change sites;
• verifies matched context against current source_of_truth files and defines a live-search fallback for unmatched questions;
• adds the simulation-system topic and refreshes the rl-learning topic;
• synchronizes the canonical skill, adapters, contributor guidance, and project agent instructions;
• adds focused validation for the context map, topic paths, routing ownership, and adapter references.

This makes common questions such as “where is this configured?” usable without requiring an explicit “reference project context” prompt.

Issue: none.

Dependencies: none.

Type of change

• Bug fix (non-breaking change which fixes an issue)
• Enhancement (non-breaking change which improves an existing functionality)
• New feature (non-breaking change which adds functionality)
• Breaking change (existing functionality will not work without user modification)
• Documentation update

Screenshots

Not applicable; this change has no visual surface.

Validation

• black --check --diff --color ./ — 667 files unchanged
• black . — 667 files unchanged
• pytest -q tests/test_agent_context_map.py — 8 passed
• git diff --check

The full pytest suite and Sphinx build were not run because runtime code, dependencies, test configuration, and docs/source/ are unchanged.

Checklist

• I have run the black . command to format the code base.
• I have made corresponding changes to the documentation.
• I have added tests that prove the change is effective.
• Dependencies have been updated, if applicable (not applicable).

[greptile-apps]

Greptile Summary

The PR expands the canonical project-context skill to support live codebase navigation and keeps its adapters and contributor guidance synchronized.

• Adds navigation routing with source-of-truth verification and live-search fallback.
• Registers a new simulation-system topic and refreshes RL pipeline guidance.
• Adds focused validation for map schema, registered paths, topic relationships, routing ownership, and adapter references.

Confidence Score: 5/5

The PR appears safe to merge with no concrete blocking or independently actionable non-blocking issues identified.

The changed routing documentation, context-map entries, simulation and RL guidance, adapters, and focused validation are internally consistent and align with the inspected source behavior.

Important Files Changed

Filename	Overview
.agents/skills/project-dev-context/SKILL.md	Defines the new navigation operation, source verification, unmatched live-search fallback, and answer contract.
agent_context/MAP.yaml	Registers simulation-system, expands RL routing metadata, and links simulation context to related topics.
agent_context/topics/simulation-system/simulation-system.md	Adds source-aligned guidance for simulation ownership, lifecycle, configuration, extension sites, and cleanup.
agent_context/topics/rl-learning/rl-learning.md	Refreshes RL navigation around CLI/config resolution, environment paths, rollout routing, distributed behavior, examples, and extension points.
tests/test_agent_context_map.py	Validates registry schema, path existence, topic references, required operational sections, representative routing ownership, and canonical adapter links.
AGENTS.md	Synchronizes repository-level navigation instructions and updates the documented project structure.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
A[Development or navigation request] --> B[Read agent_context/MAP.yaml]
B --> C{Topic matches id, alias, or keyword?}
C -->|Yes: read| D[Load mapped topic paths]
C -->|Yes: navigate| E[Load topic and verify source_of_truth]
C -->|No: navigate| F[Search working tree with rg]
E --> G[Report owner, resolution path, change site, and validation]
F --> G
C -->|Refresh or add| H[Read source and context conventions]
H --> I[Update topic and registry]

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