Project configuration does not load: trust the repository in Codex, then
start a new session if needed.
Context7 is unavailable or unauthenticated: it is optional. Export
CONTEXT7_API_KEY from the parent process or use approved authentication; do not
add a substitute MCP server.
Repository skills are not visible: start a new Codex session after adding or
changing skills.
Serena or Graphify is unavailable: phase 2 is not installed. Phase 1 provides
no bootstrap or runtime.
Generated artifacts need cleanup: remove only known derived paths. Confirm
targets before cleanup and never delete canonical schemas, templates, catalog,
installers, libraries, prompts, tests, docs, or agent assets.
Phase 2 troubleshooting
A missing mount is fatal; do not replace it with a workspace directory.
A missing language server is a build defect; runtime npm, uvx, PowerShell
module installation, and downloader fallbacks are forbidden.
Doctor reports only. It must not repair permissions, seed volumes, or write
configuration.
Serena configuration writes indicate an incomplete or migrated tracked
configuration and must fail validation. Both YAML files must retain identical
bytes and timestamps across load and pre-registered startup.
Graphify clean refuses any output path that is not the exact nested mount and
never follows symlinks.