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.
On reinstall (EXISTING=1), read the old .core-manifest and deprecate
any agent that is no longer shipped in the repo, before writing the
new manifest. Prevents stale core agents from lingering in the vault.
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
- Fix call-chain example consistency in CLAUDE.md and agent-orchestration.md
(chain lists already-invoked agents, "step N" matches chain length + 1)
- Renumber architect.md Task Checklist (was skipping 3) and replace
"Leave messages" step with dispatcher-driven "Suggested next agent"
- Replace "Leave a message to the Sorter" with signal via Suggested next agent
- Clarify "Do NOT write to other agents' files" → only prompt/config files
(.claude/agents/*.md), normal vault edits still allowed
- Fix agent count 10→8 in docs/getting-started.md
- Initialize SKILL_COUNT before conditional block in launchme.sh
