fix: flip symlink structure - AGENTS.md is the real file

AGENTS.md is now the canonical instruction file, with CLAUDE.md,
.cursorrules, and .github/copilot-instructions.md as symlinks to it.

This is simpler and more intuitive - the main file is at the root,
not buried in .github/.

Updated all references across agents, commands, skills, and .memory/.

.config/opencode/commands/bootstrap-memory.md

@@ -29,7 +29,7 @@ Run `git ls-files` to understand the project layout, then read `README.md` and
 the highest-signal files for architecture and conventions.
 
 Also check for existing cross-tool instruction files (`AGENTS.md`, `CLAUDE.md`,
-`.github/copilot-instructions.md`, `.cursorrules`) — they may contain project
+`.cursorrules`, `.github/copilot-instructions.md`) — they may contain project
 knowledge from other tools or team members that should be incorporated.
 
 Identify:
@@ -62,9 +62,10 @@ constraints). Include rationale when known.
 
 ## Step 6: Update instruction file
 
-If `.github/copilot-instructions.md` exists, update it with any new project knowledge
-discovered during bootstrap (architecture, conventions, commands). The symlinks
-(`AGENTS.md`, `CLAUDE.md`, `.cursorrules`) will automatically reflect changes.
+If `AGENTS.md` exists, update it with any new project knowledge discovered
+during bootstrap (architecture, conventions, commands). The symlinks
+(`CLAUDE.md`, `.cursorrules`, `.github/copilot-instructions.md`) will
+automatically reflect changes.
 
 If the instruction file doesn't exist, note that `/init` should be run to create it.
 

.config/opencode/commands/init.md

@@ -45,10 +45,10 @@ 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
-  - `.github/copilot-instructions.md` — real instruction file containing shared project guidance
-  - `AGENTS.md` — symlink to `.github/copilot-instructions.md`
-  - `CLAUDE.md` — symlink to `.github/copilot-instructions.md`
-  - `.cursorrules` — symlink to `.github/copilot-instructions.md`
+  - `AGENTS.md` — real instruction file containing shared project guidance
+  - `CLAUDE.md` — symlink to `AGENTS.md`
+  - `.cursorrules` — symlink to `AGENTS.md`
+  - `.github/copilot-instructions.md` — symlink to `../AGENTS.md`
   - `docs/architecture.md` — stub with title + purpose
   - `.gitignore` — add stack-appropriate ignores (e.g., `node_modules/`, `__pycache__/`, `target/`)
   - `.memory/` — create and/or update `knowledge.md`, `decisions.md`, `plans/`, `research/`
@@ -59,15 +59,15 @@ 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
-  - ensure `.github/copilot-instructions.md` exists as the real instruction file
+  - ensure `AGENTS.md` exists as the real instruction file
   - create missing symlinks:
-    - `ln -s .github/copilot-instructions.md AGENTS.md`
-    - `ln -s .github/copilot-instructions.md CLAUDE.md`
-    - `ln -s .github/copilot-instructions.md .cursorrules`
-  - if `.github/copilot-instructions.md` is missing but `AGENTS.md` exists as a real file, move AGENTS content into `.github/copilot-instructions.md`, then recreate `AGENTS.md` as a symlink
+    - `ln -s AGENTS.md CLAUDE.md`
+    - `ln -s AGENTS.md .cursorrules`
+    - `ln -s ../AGENTS.md .github/copilot-instructions.md`
+  - if `AGENTS.md` is missing but `.github/copilot-instructions.md` exists as a real file, move its content into `AGENTS.md`, then recreate `.github/copilot-instructions.md` as a symlink
   - if `.memory/` is missing, create the full `.memory/` directory structure
   - examples:
-    - if `README.md` exists and only `AGENTS.md` is missing, create `AGENTS.md` as a symlink to `.github/copilot-instructions.md`
+    - if `README.md` exists and only `CLAUDE.md` is missing, create `CLAUDE.md` as a symlink to `AGENTS.md`
     - if `docs/` is missing, create it and add `docs/architecture.md`
 
 ## Step 4 — Documentation review (delegate to `librarian`)
@@ -75,8 +75,8 @@ Delegate to the `coder` subagent with explicit mode (`new_project` or `existing_
 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 `.github/copilot-instructions.md` exists and captures project-specific workflow decisions from Step 2.
-- Verify `AGENTS.md`, `CLAUDE.md`, and `.cursorrules` are symlinks to `.github/copilot-instructions.md`.
+- Ensure `AGENTS.md` exists and captures project-specific workflow decisions from Step 2.
+- Verify `CLAUDE.md`, `.cursorrules`, and `.github/copilot-instructions.md` are symlinks to `AGENTS.md`.
 - Ensure stubs are explicitly marked for later completion.
 - Keep edits additive and non-destructive for existing projects.
 

.config/opencode/commands/save-memory.md

@@ -58,8 +58,8 @@ Report what was added/updated and where.
 ## Step 6: Update instruction file if project knowledge changed
 
 If `.memory/knowledge.md` was **materially** updated (architecture, conventions,
-commands — not just plans/research), update `.github/copilot-instructions.md` to
-reflect the changes. The symlinks automatically propagate to all tools.
+commands — not just plans/research), update `AGENTS.md` to reflect the changes.
+The symlinks automatically propagate to all tools.
 
 If updates were only plans/research/tracking details, skip this step.