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Background agents running queued tasks in a project cannot read files outside the project directory (e.g. /storage/share/codelib/**) or use sirocampus MCP tools, because .claude/settings.json only allows reads within the project root.

Current workaround: manually added Read(/storage/share/codelib/*) and mcp__sirocampus__ to cogpy's .claude/settings.json.

What should happen: projio should manage .claude/settings.json permissions as part of project configuration, and worklog should propagate shared resource access (codelib reads, sirocampus MCP) to all projects that have codio dependencies. When a project has codio entries with runtime_import: reference_only and managed clones, the agent should automatically get read access to those paths.

Concrete requirements: 1. projio should have a permissions_sync or similar tool that writes/updates .claude/settings.json based on project config (codio deps, MCP servers, etc.) 2. worklog's enqueue_task / execute_task should ensure the target project's permissions are up-to-date before spawning the agent 3. Shared resources like /storage/share/codelib/* and mcp__sirocampus__ should be injected automatically for any project that uses codio

Source context: cogpy

CogPy (cogpy): ECoG Analysis Python library

Recent commits: 

7e39755 fix CI docs build: install all extras, register cogpy Jupyter kernel
e9fa999 switch GitHub Pages workflow from mkdocs to Sphinx, fix README doc links
7ccbf7d update README and pyproject.toml links to GitHub, fix pip install name to ecogpy

README:

cogpy

Atomic, composable primitives for ECoG / iEEG signal processing.

Python 3.10+ License: MIT

**[Documentation](https://arashshahidi1997.github.io/cogp

  • [[docs/log/issue/issue-arash-20260331-172325-785765.md]] — Agent safety settings are directly related to managing .claude/settings.json permissions for background agents
  • [[docs/log/issue/issue-arash-20260331-171537-647473.md]] — Adding projio claude update hook scaffolding overlaps with the requirement for projio to manage .claude/settings.json as part of project configuration
  • [[docs/log/issue/issue-arash-20260327-141525-036428.md]] — Same pattern: injecting shared external resources (git-annex PATH) into agent environment — a parallel to injecting codelib read permissions
  • [[docs/log/issue/issue-arash-20260327-155921-977015.md]] — Codio RAG sync issues are relevant since the permissions note ties read-access propagation to projects with codio dependencies