neotoma 0.3.0 → 0.3.2

package/.cursor/commands/run_feature_workflow.md

@@ -1,83 +0,0 @@
-<!--
-⚠️  DO NOT EDIT THIS FILE DIRECTLY
-
-This is a copy of: foundation/agent_instructions/cursor_commands/run_feature_workflow.md
-Source of truth: foundation/agent_instructions/cursor_commands/run_feature_workflow.md
-
-To edit this command:
-1. Edit the source file in foundation: foundation/agent_instructions/cursor_commands/run_feature_workflow.md
-2. Run '/setup_cursor_copies' to sync changes
-
-This file will be overwritten when running setup_cursor_copies.
--->
-
-# Run Feature Workflow
-
-feature_id = {{input:feature_id}}
-
-Configuration is read from `foundation-config.yaml`.
-
-1. **Load configuration:**
-   - Read `foundation-config.yaml` to get feature unit settings
-   - Determine directory structure, manifest complexity, testing requirements
-
-2. **Read authoritative documents:**
-   - `foundation/development/feature_unit_workflow.md` (workflow context)
-   - `{configured_directory}/in_progress/{{input:feature_id}}/{{input:feature_id}}_spec.md` (or `completed/` if completed)
-   - `{configured_directory}/in_progress/{{input:feature_id}}/manifest.yaml` (or `completed/` if completed)
-   - `foundation/development/templates/feature_unit_spec_template.md`
-   - Repository-specific execution instructions (if they exist)
-   - Repository-specific architecture/module documentation (based on spec)
-
-3. **Determine risk level:**
-   - low → skip plan
-   - medium → produce brief structured plan
-   - high/critical → produce detailed plan and wait for user approval
-
-4. **Apply Feature Unit execution principles:**
-   - Update spec/manifest if ambiguous
-   - Update code/tests/docs together
-   - Follow architectural invariants (from repo-specific docs)
-   - Preserve accessibility and i18n rules (if applicable)
-
-5. **Run tests (based on configuration):**
-   - Unit tests (if `testing.require_unit_tests: true`)
-   - Integration tests (if `testing.require_integration_tests: true`)
-   - E2E tests (if `testing.require_e2e_tests: true`)
-   - Verify coverage meets configured targets
-   
-   **If any tests fail:**
-   - Immediately invoke `Fix Feature Bug` with feature_id={{input:feature_id}}
-   - Do NOT attempt to fix bugs inline
-   - Let the error protocol classify and correct
-   - After bugfix completes, re-run the test suite
-   - Only proceed to step 6 once all tests pass
-
-6. **Apply error protocol** (if repository has one) only if bugs were encountered and fixed via step 5.
-
-7. **Spec-to-Implementation Diff Checkpoint (CRITICAL):**
-
-   Before producing the final summary:
-   
-   - Compare the implemented code against the spec
-   - List any ways implementation **intentionally diverged** from spec (even if small)
-   - For each divergence:
-     - Either update the spec to reflect the change (if divergence is intentional and correct)
-     - Or mark the divergence as a bug to be fixed (if divergence is unintentional)
-   - Present this diff to the user:
-     - "Implementation vs Spec Diff: [list of divergences]"
-     - "For each divergence, should I update the spec or fix the implementation? (spec/implementation/list)"
-   - Do NOT proceed to final summary until spec and implementation are aligned (either by updating spec or fixing implementation)
-
-8. **Produce a final change summary:**
-   - feature_id
-   - files changed
-   - risk
-   - error_class (if bugfix)
-   - tests run
-   - coverage achieved
-
-## Inputs
-
-- `feature_id` (string): The feature_id to work on.
-

package/.cursor/commands/setup_commands.md

@@ -1,87 +0,0 @@
-<!--
-⚠️  DO NOT EDIT THIS FILE DIRECTLY
-
-This is a copy of: foundation/agent_instructions/cursor_commands/setup_commands.md
-Source of truth: foundation/agent_instructions/cursor_commands/setup_commands.md
-
-To edit this command:
-1. Edit the source file in foundation: foundation/agent_instructions/cursor_commands/setup_commands.md
-2. Run '/setup_cursor_copies' to sync changes
-
-This file will be overwritten when running setup_cursor_copies.
--->
-
-# Setup Foundation Commands Only
-
-Sets up symlinks from foundation cursor **commands** to `.cursor/commands/`. Does not link or change rules.
-
-## Command
-
-```
-setup_commands
-```
-
-or
-
-```
-setup commands
-```
-
-## Purpose
-
-This command runs `foundation/scripts/setup_cursor_commands.sh`, which:
-
-1. Creates symlinks from `foundation/agent_instructions/cursor_commands/` to `.cursor/commands/`
-2. Uses original filenames (no prefix)
-3. Removes existing foundation command symlinks before creating new ones
-4. Preserves non-symlink files (e.g. repo-specific commands like `migrate_plans.md`)
-5. **Does not touch** `.cursor/rules/` or repo rules from `docs/`
-
-Use this when you only want foundation commands (e.g. commit, pull, push) without linking rules. Use `/setup_symlinks` to link both rules and commands.
-
-## When to Use
-
-- When you want foundation commands (commit, pull, push, etc.) but keep repo-specific rules
-- After updating the foundation submodule and you only need commands refreshed
-- When rules are managed separately (e.g. via setup_cursor_copies)
-
-## Execution Instructions
-
-### Step 1: Verify Foundation Directory
-
-- Look for `foundation/` in repo root, or `../foundation/` if in a subdirectory
-- If not found, error: "Foundation directory not found. Please ensure foundation is installed."
-
-### Step 2: Run Setup Script
-
-**Execute:**
-
-```bash
-./foundation/scripts/setup_cursor_commands.sh
-```
-
-**Or if foundation is in parent directory:**
-
-```bash
-../foundation/scripts/setup_cursor_commands.sh
-```
-
-### Step 3: Verify Results
-
-- Check `.cursor/commands/` for symlinks to foundation commands (e.g. `commit.md`, `pull.md`, `push.md`)
-- Repo-specific command files (e.g. `migrate_plans.md`) are left unchanged
-- `.cursor/rules/` is not modified
-
-## What Gets Created
-
-**Symlinks in `.cursor/commands/`:**
-
-- `commit.md` → `foundation/agent_instructions/cursor_commands/commit.md`
-- `pull.md` → `foundation/agent_instructions/cursor_commands/pull.md`
-- `push.md` → `foundation/agent_instructions/cursor_commands/push.md`
-- ... (all other foundation commands, same filenames)
-
-## Related
-
-- **Setup rules and commands:** `/setup_symlinks` runs `setup_cursor_rules.sh` (rules + commands + repo rules from docs)
-- **Foundation commands source:** `foundation/agent_instructions/cursor_commands/`

package/.cursor/commands/setup_symlinks.md

@@ -1,234 +0,0 @@
-<!--
-⚠️  DO NOT EDIT THIS FILE DIRECTLY
-
-This is a copy of: foundation/agent_instructions/cursor_commands/setup_symlinks.md
-Source of truth: foundation/agent_instructions/cursor_commands/setup_symlinks.md
-
-To edit this command:
-1. Edit the source file in foundation: foundation/agent_instructions/cursor_commands/setup_symlinks.md
-2. Run '/setup_cursor_copies' to sync changes
-
-This file will be overwritten when running setup_cursor_copies.
--->
-
-# Setup Foundation Symlinks
-
-Sets up symlinks from foundation cursor rules and commands to `.cursor/` directory.
-
-## Command
-
-```
-setup_symlinks
-```
-
-or
-
-```
-setup symlinks
-```
-
-## Purpose
-
-This command runs the foundation symlinks script (`foundation/scripts/setup-cursor-rules.sh`) which:
-
-1. Creates symlinks from `foundation/agent_instructions/cursor_rules/` to `.cursor/rules/`
-2. Creates symlinks from `foundation/agent_instructions/cursor_commands/` to `.cursor/commands/`
-3. Uses original filenames (no prefix)
-4. Removes existing foundation symlinks before creating new ones
-5. Preserves any non-symlink files (custom rules/commands)
-
-**When run from the foundation repository itself**, it also automatically runs the setup script in peer repositories (located at `../*`) that include this foundation repo via symlink.
-
-## When to Use
-
-- After installing foundation for the first time
-- After updating foundation submodule (to refresh symlinks)
-- When cursor rules/commands are not working (symlinks may be broken)
-- When you want to ensure symlinks are up to date
-
-## Execution Instructions
-
-### Step 1: Verify Foundation Directory
-
-**Check if foundation exists:**
-
-- Look for `foundation/` directory in repo root
-- If not found, check `../foundation/` (parent directory)
-- If still not found, error: "Foundation directory not found. Please ensure foundation is installed."
-
-### Step 2: Run Setup Script in Current Repository
-
-**Execute the script:**
-
-```bash
-./foundation/scripts/setup-cursor-rules.sh
-```
-
-**Or if foundation is in parent directory:**
-
-```bash
-../foundation/scripts/setup-cursor-rules.sh
-```
-
-### Step 3: Run Setup Script in Peer Repositories (If in Foundation Repo)
-
-**If running from the foundation repository itself** (detected by presence of `agent_instructions/cursor_commands/` directory):
-
-1. **Get current repository absolute path:**
-   ```bash
-   CURRENT_REPO=$(pwd -P)
-   ```
-
-2. **Find peer repositories in parent directory:**
-   ```bash
-   PARENT_DIR=$(dirname "$CURRENT_REPO")
-   for peer_repo in "$PARENT_DIR"/*; do
-     # Skip if not a directory or if it's the current repo
-     if [ ! -d "$peer_repo" ] || [ "$peer_repo" = "$CURRENT_REPO" ]; then
-       continue
-     fi
-     
-     # Check if peer repo has foundation/ symlink pointing to this repo
-     if [ -L "$peer_repo/foundation" ]; then
-       SYMLINK_TARGET=$(readlink -f "$peer_repo/foundation" 2>/dev/null || readlink "$peer_repo/foundation")
-       if [ "$SYMLINK_TARGET" = "$CURRENT_REPO" ]; then
-         echo "Found peer repo with foundation symlink: $(basename "$peer_repo")"
-         # Run setup script in peer repo using absolute path
-         (cd "$peer_repo" && "$CURRENT_REPO/scripts/setup_cursor_rules.sh" || echo "Failed to run in $(basename "$peer_repo")")
-       fi
-     fi
-   done
-   ```
-
-**Behavior:**
-- Only runs in peer repos if executing from foundation repo itself
-- Detects peer repos by checking `../*` directories
-- Verifies each peer repo has `foundation/` symlink pointing to current repo
-- Runs setup script in each matching peer repo
-- Continues even if one peer repo fails
-
-**Expected output (when peer repos found):**
-```
-[INFO] Setting up cursor rules and commands...
-...
-[INFO] ✅ Cursor rules setup complete!
-
-[INFO] Detected foundation repository - checking for peer repos...
-[INFO] Found peer repo with foundation symlink: my-project
-[INFO] Running setup script in my-project...
-[INFO] Setting up cursor rules and commands...
-...
-[INFO] ✅ Cursor rules setup complete!
-[INFO] ✓ Successfully updated my-project
-
-[INFO] Updated 1 peer repo(s)
-```
-
-### Step 4: Verify Results
-
-**Check output:**
-
-- Script should report number of rules linked
-- Script should report number of commands linked
-- Check `.cursor/rules/` for foundation rule symlinks (using original filenames)
-- Check `.cursor/commands/` for foundation command symlinks (using original filenames)
-
-**Expected output:**
-
-```
-[INFO] Setting up cursor rules and commands...
-[INFO] Foundation directory: foundation
-[INFO] Creating symlinks for generic cursor rules...
-  ✓ Linked security.mdc
-  ✓ Linked worktree_env.mdc
-  ...
-[INFO] Creating symlinks for generic cursor commands...
-  ✓ Linked commit.md
-  ✓ Linked analyze.md
-  ...
-[INFO] ✅ Cursor rules setup complete!
-[INFO]   Rules linked: X
-[INFO]   Commands linked: Y
-```
-
-## What Gets Created
-
-**Symlinks in `.cursor/rules/`:**
-- `security.mdc` → `foundation/agent_instructions/cursor_rules/security.mdc`
-- `worktree_env.mdc` → `foundation/agent_instructions/cursor_rules/worktree_env.mdc`
-- `readme_maintenance.mdc` → `foundation/agent_instructions/cursor_rules/readme_maintenance.mdc`
-- ... (all rules from foundation, using original filenames)
-
-**Symlinks in `.cursor/commands/`:**
-- `commit.md` → `foundation/agent_instructions/cursor_commands/commit.md`
-- `analyze.md` → `foundation/agent_instructions/cursor_commands/analyze.md`
-- ... (all commands from foundation, using original filenames)
-
-## Behavior
-
-**Filenames:**
-- Symlinks use original filenames from foundation (no prefix)
-- Example: `security.mdc` remains `security.mdc`
-
-**Existing Files:**
-- If a file already exists (not a symlink), it's preserved
-- Script skips creating symlink to preserve customizations
-- To replace with foundation version, manually remove the file first
-
-**Existing Symlinks:**
-- All existing foundation symlinks (old prefixed and new unprefixed) are removed first
-- New symlinks are created fresh with original filenames
-- Ensures symlinks point to current foundation version
-
-## Error Handling
-
-### Foundation Directory Not Found
-
-**Error:**
-```
-[ERROR] Foundation directory not found. Please run from repository root or ensure foundation is installed.
-```
-
-**Solution:**
-- Ensure you're in repository root
-- Verify foundation is installed (as submodule or symlink)
-- Check if foundation is in parent directory
-
-### Cursor Rules Directory Not Found
-
-**Error:**
-```
-[ERROR] Cursor rules directory not found: foundation/agent_instructions/cursor_rules
-```
-
-**Solution:**
-- Verify foundation submodule is initialized: `git submodule update --init`
-- Check that foundation has cursor rules directory
-
-### Cursor Commands Directory Not Found
-
-**Error:**
-```
-[ERROR] Cursor commands directory not found: foundation/agent_instructions/cursor_commands
-```
-
-**Solution:**
-- Verify foundation submodule is initialized: `git submodule update --init`
-- Check that foundation has cursor commands directory
-
-## Related Documents
-
-- `foundation/scripts/setup-cursor-rules.sh` - The script that performs the setup
-- `foundation/agent_instructions/README.md` - Cursor rules and commands documentation
-- `foundation/README.md` - Foundation overview and installation
-
-## Notes
-
-- This command is generic and works for any repo using foundation as submodule
-- Symlinks ensure single source of truth (foundation)
-- Updates to foundation automatically apply to symlinked rules/commands
-- Custom rules/commands (non-symlink files) are preserved
-- Uses original filenames (no prefix) - repository-specific rules use different naming patterns
-- **When run from foundation repo**: Automatically propagates to peer repos that symlink to this foundation
-- **Peer repo detection**: Only processes repos in `../*` that have `foundation/` symlink pointing to this repo
-