feat: replace megamemory with markdown-based memory system

Remove the megamemory MCP knowledge graph and replace with plain
markdown files in .memory/ for tracking plans, research, knowledge,
and implementation state. This enables collaboration across people
and agentic coding tools (Claude Code, Copilot, Cursor, etc.).

Changes:
- Remove megamemory MCP from opencode.jsonc
- Delete tool/megamemory.ts and .megamemory/ database
- Rewrite all 25 config files to use .memory/ markdown files
- Add cross-tool instruction file awareness (AGENTS.md, CLAUDE.md,
  copilot-instructions.md, .cursorrules)
- Update save-memory, bootstrap-memory, status commands for md workflow
- Update all agent files, skills, and commands consistently

.config/opencode/agents/librarian.md

@@ -18,13 +18,13 @@ Purpose:
 
 Operating rules:
 
-1. Query megamemory with `megamemory:understand` (`top_k=3`) when relevant concepts likely exist; skip when `list_roots` already showed no relevant concepts in this domain this session; never re-query concepts you just created.
+1. Read relevant `.memory/*.md` files when prior context likely exists; skip when this domain already has no relevant `.memory/` entries this session.
 2. Review the implemented changes and update docs accordingly:
    - `README`
    - relevant `docs/*`
    - `AGENTS.md` when workflow, policy, or agent behavior changes.
 3. If documentation scope is ambiguous, use the `question` tool.
-4. Record documentation outcomes and any deferred gaps in megamemory (create/update/link), including file refs and rationale.
+4. Record documentation outcomes and any deferred gaps in the relevant `.memory/` files, including file refs, rationale, and markdown cross-references.
 5. Recording discipline: record only outcomes/discoveries/decisions, never phase-transition or ceremony checkpoints.
 6. Do not run shell commands.