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/commands/init.md

@@ -1,5 +1,5 @@
 ---
-description: Initialize or update a project with scaffold, docs, and knowledge graph — adapts to both new and existing projects.
+description: Initialize or update a project with scaffold, docs, and .memory files — adapts to both new and existing projects.
 ---
 
 You are initializing or updating a project. Follow these steps in order.
@@ -46,8 +46,12 @@ Delegate to the `coder` subagent with explicit mode (`new_project` or `existing_
 - Required scaffold targets:
   - `README.md` — title, purpose, tech stack, quick-start, project structure overview
   - `AGENTS.md` — project-specific workflow notes (code style, test commands, linting, build commands, commit conventions); do **not** duplicate global `AGENTS.md` policies — only add project-specific details
+  - `CLAUDE.md` — project instructions for Claude Code (same core content as `AGENTS.md`, adapted for Claude)
+  - `.github/copilot-instructions.md` — project instructions for GitHub Copilot
+  - `.cursorrules` — project instructions for Cursor
   - `docs/architecture.md` — stub with title + purpose
-  - `.gitignore` — must include `.megamemory/` entry; add stack-appropriate ignores (e.g., `node_modules/`, `__pycache__/`, `target/`)
+  - `.gitignore` — add stack-appropriate ignores (e.g., `node_modules/`, `__pycache__/`, `target/`)
+  - `.memory/` — create and/or update `knowledge.md`, `decisions.md`, `plans/`, `research/`
   - other stack-specific scaffold files if clearly implied (e.g., `package.json`, `pyproject.toml`)
 - If `new_project`:
   - create all required scaffold files/directories
@@ -55,7 +59,9 @@ Delegate to the `coder` subagent with explicit mode (`new_project` or `existing_
   - create or fill in only missing pieces
   - **do not overwrite existing files**
   - explicitly instruct coder to check existence before creating each target
-  - if `.gitignore` exists, instruct coder to append `.megamemory/` if not already present
+  - if any cross-tool instruction files are missing (`AGENTS.md`, `CLAUDE.md`, `.github/copilot-instructions.md`, `.cursorrules`), create them
+  - if they exist, verify they are in sync with `AGENTS.md` for core project knowledge (purpose, stack, conventions, commands, structure)
+  - if `.memory/` is missing, create the full `.memory/` directory structure
   - examples:
     - if `README.md` exists and `AGENTS.md` is missing, create only `AGENTS.md`
     - if `docs/` is missing, create it and add `docs/architecture.md`
@@ -66,21 +72,21 @@ Always delegate to the `librarian` subagent, for both new and existing projects.
 
 - Ensure `README.md` is accurate and complete for the current project state.
 - Ensure `AGENTS.md` captures project-specific workflow decisions from Step 2.
+- Verify cross-tool instruction files are consistent with each other (`AGENTS.md`, `CLAUDE.md`, `.github/copilot-instructions.md`, `.cursorrules`).
 - Ensure stubs are explicitly marked for later completion.
 - Keep edits additive and non-destructive for existing projects.
 
-## Step 5 — Initialize or update knowledge graph (Lead)
+## Step 5 — Initialize or update `.memory` project overview (Lead)
 
-Always update megamemory for this project.
+Always create or update `.memory/knowledge.md` for this project.
 
-- First call `megamemory:understand` to check whether a project root concept already exists.
-- If an appropriate concept exists, call `megamemory:update_concept`.
-- If none exists, call `megamemory:create_concept` with:
-  - Kind: `module`
-  - Name: `<project name>`
-  - Summary: purpose, stack, key files, and notable init/update decisions
-  - File refs: include whichever exist among `README.md`, `AGENTS.md`, `docs/architecture.md`
-- Create links (`megamemory:link`) from this concept to related existing concepts when applicable. If no related concepts exist yet (brand new knowledge graph), skip linking.
+- Read existing `.memory/knowledge.md` (if present) to avoid duplicate sections.
+- Create or update a project overview section with:
+  - Project name
+  - Purpose and stack
+  - Key files (`README.md`, `AGENTS.md`, `docs/architecture.md` when present)
+  - Notable init/update decisions
+- Add markdown cross-references to related sections in `.memory/decisions.md` when applicable.
 
 ## Step 6 — Git handling (delegate to `coder`)
 
@@ -88,12 +94,11 @@ Delegate git operations to `coder` based on discovered state.
 
 - If `.git/` already exists:
   - skip `git init`
-  - ensure `.megamemory/` is in `.gitignore` (if not already handled in Step 3)
   - stage only newly created or modified files from this init/update flow
   - create a commit
 - If `.git/` does not exist:
   - use Step 2 answer to decide whether to run `git init`
-  - if initialized, ensure `.megamemory/` is in `.gitignore`, then stage only newly created or modified files and create a commit
+  - if initialized, stage only newly created or modified files and create a commit
 - Commit message should be concise and conventional, e.g.:
   - `chore: initialize project scaffold` (new project)
   - `chore: add missing project scaffolding` (existing project)