Claude Code only auto-discovers “skills/agents/commands” in two places:
~/.claude/...
- a
.claude/... folder inside projects
PAI keeps its stuff under ~/REPOS/PAI/commands, ~/REPOS/PAI/skills, etc. Those aren’t either, so Claude won’t notice new files there on its own.
The symlinked settings.json created with the command below just tells Claude where to run certain scripts; it doesn’t change the auto-discovery rule.
ln -sf $PAI_DIR/settings.json ~/.claude/settings.json
Maybe I'm missing something!