Same pattern as agents: launchme/updateme write a .core-manifest in
.claude/references/ listing installed core files. The deprecation loop
only touches files in the manifest, leaving user-created references
untouched.
The manifest was being truncated and rewritten before the deprecation
loop ran, so removed core agents were no longer in the manifest and
got skipped as "custom". Now: read old manifest -> deprecate -> copy
new agents -> rewrite manifest.
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
