Deprecate removed files instead of leaving orphans in the vault

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/)

scripts/launchme.sh

@@ -163,8 +163,8 @@ echo -e "   Your vault is ready. Here's what was installed:"
 echo ""
 echo -e "   ${VAULT_DIR}/"
 echo -e "   ├── .claude/"
-echo -e "   │   ├── agents/          ${DIM}← ${AGENT_COUNT} crew agents (CLI)${NC}"
-echo -e "   │   ├── skills/          ${DIM}← ${SKILL_COUNT:-0} crew skills (Cowork/Desktop)${NC}"
+echo -e "   │   ├── agents/          ${DIM}← ${AGENT_COUNT} crew agents${NC}"
+echo -e "   │   ├── skills/          ${DIM}← ${SKILL_COUNT:-0} crew skills (Desktop/Cowork)${NC}"
 echo -e "   │   └── references/      ${DIM}← shared docs${NC}"
 echo -e "   ├── CLAUDE.md            ${DIM}← project instructions${NC}"
 if [[ "$MCP_ANSWER" =~ ^[Yy]$ ]]; then