launchme.sh and updateme.sh now write .core-manifest listing which agent
files were installed as core. The deprecation loop checks this manifest
before touching any file, so custom agents are never deprecated.
When a file is removed from the repo (agents, references, or skills),
the updater now renames it with a "-DEPRECATED" suffix and prepends
a "DEPRECATED DO NOT USE" header instead of silently leaving it.
updateme.sh:
- Core agents in .claude/agents/ that no longer exist in the repo
get renamed to {name}-DEPRECATED.md with deprecation header
(custom agents are never touched)
- References in .claude/references/ that no longer exist in the repo
get the same treatment
- The entire .claude/skills/ directory (removed from the project)
gets renamed to .claude/skills-DEPRECATED/ with deprecation headers
on each SKILL.md
- Summary now reports deprecated file count
launchme.sh:
- Added confirmation prompt before overwriting existing installation
- Skills generation and copying kept intact (generate-skills.py runs
first, then copies to .claude/skills/)
launchme.sh:
- Detects if .claude/ or CLAUDE.md already exist in the vault
- Shows the user what will be overwritten
- Asks for explicit confirmation before proceeding
- Clarifies that custom agents and vault notes are never touched
updateme.sh:
- Asks for confirmation before overwriting core files
- Same clarification about custom agents being preserved
- generate-skills.py now respects SKILLS_DIR env var
- launchme.sh and updateme.sh generate into mktemp -d, copy to vault,
then clean up — no more untracked skills/ left in the repo
- Warn the user when python3 is missing so Cowork/Desktop users know
why .claude/skills/ is absent
