neotoma 0.3.0 → 0.3.2

package/.claude/skills/pull.md

@@ -1,314 +0,0 @@
----
-name: pull
-description: pull
----
-
-<!-- Source: foundation/agent_instructions/cursor_commands/pull.md -->
-
-# pull
-
-Pull latest commits from origin, committing local changes first, merging conflicts, and running setup scripts.
-
-**SUBMODULE MODE**: If a submodule name is provided (e.g., `/pull foundation`), scope operations to that submodule only, not the main repository.
-
-Configuration is read from `foundation-config.yaml`.
-
-If submodule name provided:
-1. Check if submodule exists: `git submodule status <submodule-name>`
-2. Change to submodule directory: `cd <submodule-name>`
-3. Run pull workflow in submodule context
-4. Exit after submodule pull (do NOT pull main repository)
-
-If no submodule name provided, proceed with main repository pull workflow below.
-
-## Workflow Overview
-
-1. Commit local changes using foundation commit command (if any uncommitted changes)
-2. Fetch latest from origin
-3. Pull latest commits (merge or rebase based on configuration)
-4. Resolve merge conflicts if they occur
-5. Run setup scripts as needed
-
-## Tasks
-
-### Step 1: Determine Scope
-
-If submodule name provided:
-1. Verify submodule exists:
-   ```bash
-   if ! git submodule status <submodule-name> >/dev/null 2>&1; then
-     echo "❌ Submodule not found: <submodule-name>"
-     exit 1
-   fi
-   ```
-
-2. Save parent directory and change to submodule directory:
-   ```bash
-   ORIGINAL_DIR=$(pwd)  # Save parent directory before cd
-   cd <submodule-name> || exit 1
-   ```
-
-3. Update scope context (all subsequent operations in submodule)
-
-If no submodule name provided, proceed with main repository context.
-
-### Step 2: Check for Uncommitted Changes
-
-```bash
-# Check if there are uncommitted changes
-if git status --porcelain | grep -q .; then
-  echo "📝 Found uncommitted changes, committing first..."
-  
-  # Use foundation commit command to commit changes
-  # Agent should invoke the commit command workflow:
-  # - Run security audit
-  # - Stage changes
-  # - Generate commit message
-  # - Commit changes
-  # - Push to origin if configured
-  
-  # For agent: Use the foundation commit command workflow
-  # Invoke: `/commit <submodule-name>` (if submodule) or `/commit` (if main repo)
-  
-  echo "✅ Local changes committed"
-else
-  echo "✅ No uncommitted changes"
-fi
-```
-
-**Agent Instructions for Commit Step:**
-- If uncommitted changes exist, invoke the foundation commit command workflow
-- If in submodule mode: use `/commit <submodule-name>`
-- If in main repo mode: use `/commit`
-- Do NOT proceed to pull until commit completes successfully
-
-### Step 3: Fetch Latest from Origin
-
-```bash
-echo "🔄 Fetching latest from origin..."
-git fetch origin
-
-# Check current branch
-CURRENT_BRANCH=$(git branch --show-current)
-
-if [ -z "$CURRENT_BRANCH" ]; then
-  echo "⚠️  Detached HEAD state - cannot pull"
-  echo "Current commit: $(git rev-parse HEAD)"
-  exit 1
-fi
-
-echo "📍 Current branch: $CURRENT_BRANCH"
-```
-
-### Step 4: Check if Pull is Needed
-
-```bash
-# Check if local branch is behind remote
-LOCAL=$(git rev-parse @)
-REMOTE=$(git rev-parse @{u} 2>/dev/null || echo "")
-
-if [ -z "$REMOTE" ]; then
-  echo "⚠️  No upstream branch set for $CURRENT_BRANCH"
-  echo "Setting upstream to origin/$CURRENT_BRANCH"
-  git branch --set-upstream-to=origin/$CURRENT_BRANCH $CURRENT_BRANCH
-  REMOTE=$(git rev-parse @{u})
-fi
-
-BASE=$(git merge-base @ @{u})
-
-if [ "$LOCAL" = "$REMOTE" ]; then
-  echo "✅ Already up to date with origin/$CURRENT_BRANCH"
-  SKIP_PULL=true
-elif [ "$LOCAL" = "$BASE" ]; then
-  echo "⬇️  Local branch is behind origin/$CURRENT_BRANCH - will pull"
-  SKIP_PULL=false
-elif [ "$REMOTE" = "$BASE" ]; then
-  echo "⬆️  Local branch is ahead of origin/$CURRENT_BRANCH"
-  SKIP_PULL=true
-else
-  echo "🔀 Local and remote branches have diverged - will pull and merge"
-  SKIP_PULL=false
-fi
-```
-
-### Step 5: Pull and Merge
-
-If `SKIP_PULL` is false:
-
-```bash
-echo "⬇️  Pulling latest changes from origin/$CURRENT_BRANCH..."
-
-# Pull with merge strategy (default)
-# If conflicts occur, git pull will pause
-git pull origin "$CURRENT_BRANCH" || {
-  PULL_EXIT_CODE=$?
-  
-  if [ $PULL_EXIT_CODE -ne 0 ]; then
-    echo "⚠️  Pull encountered issues"
-    
-    # Check if there are merge conflicts
-    if git status | grep -q "Unmerged paths"; then
-      echo "🔀 Merge conflicts detected"
-      echo ""
-      echo "Conflicted files:"
-      git status | grep "both modified\|both added\|deleted by them\|deleted by us" || true
-      echo ""
-      
-      # Agent should resolve conflicts interactively
-      # For now, list conflicts and ask user
-      echo "❌ Merge conflicts must be resolved manually"
-      echo "Run 'git status' to see conflicted files"
-      echo "Resolve conflicts, then run 'git add <file>' for each resolved file"
-      echo "Finally, run 'git commit' to complete the merge"
-      exit 1
-    else
-      echo "❌ Pull failed for unknown reason"
-      exit 1
-    fi
-  fi
-}
-
-echo "✅ Successfully pulled latest changes"
-```
-
-**Agent Instructions for Conflict Resolution:**
-- If merge conflicts occur, DO NOT attempt automatic resolution
-- List all conflicted files to user
-- Ask user how to proceed: resolve manually, abort merge, or use specific merge strategy
-- If user chooses to resolve manually, pause and wait for user to complete resolution
-- After user indicates conflicts are resolved, verify with `git status`
-- Stage resolved files with `git add`
-- Complete merge with `git commit`
-
-### Step 6: Detect and Run Setup Scripts
-
-After successful pull, detect and run setup scripts as needed:
-
-**IMPORTANT**: If in submodule mode, return to parent repository directory BEFORE running setup scripts, as parent-level setup scripts (like `foundation/scripts/setup_cursor_rules.sh`) must be run from the parent repository context.
-
-```bash
-echo "🔧 Checking for setup scripts..."
-
-# If in submodule mode, return to parent directory for setup scripts
-if [ -n "$ORIGINAL_DIR" ]; then
-  echo "📁 Returning to parent repository for setup scripts..."
-  cd "$ORIGINAL_DIR" || exit 1
-fi
-
-# Common setup script patterns
-SETUP_SCRIPTS=()
-
-# Check for foundation setup script (must run from parent repo)
-if [ -f "foundation/scripts/setup_cursor_rules.sh" ]; then
-  SETUP_SCRIPTS+=("foundation/scripts/setup_cursor_rules.sh")
-fi
-
-# Check for foundation validation script
-if [ -f "foundation/scripts/validate_setup.sh" ]; then
-  SETUP_SCRIPTS+=("foundation/scripts/validate_setup.sh")
-fi
-
-# Check for repository-specific setup scripts
-if [ -f "scripts/setup_agent_environment.sh" ]; then
-  SETUP_SCRIPTS+=("scripts/setup_agent_environment.sh")
-fi
-
-# Check for other common setup scripts
-for script in scripts/setup*.sh scripts/*setup*.sh; do
-  if [ -f "$script" ] && [ -x "$script" ]; then
-    if [[ ! " ${SETUP_SCRIPTS[@]} " =~ " ${script} " ]]; then
-      SETUP_SCRIPTS+=("$script")
-    fi
-  fi
-done
-
-# Check package.json for setup/install scripts
-if [ -f "package.json" ]; then
-  echo "📦 Checking package.json for setup requirements..."
-  
-  # Check if node_modules exists
-  if [ ! -d "node_modules" ]; then
-    echo "📦 node_modules not found - running npm install..."
-    npm install
-  else
-    # Check if package.json or package-lock.json changed
-    if git diff HEAD@{1} HEAD --name-only | grep -q "package.json\|package-lock.json"; then
-      echo "📦 Dependencies may have changed - running npm install..."
-      npm install
-    fi
-  fi
-fi
-
-# Check for other package managers
-if [ -f "requirements.txt" ] && [ ! -d "venv" ] && [ ! -d ".venv" ]; then
-  echo "🐍 Python dependencies detected - consider setting up virtual environment"
-fi
-
-# Run setup scripts
-for script in "${SETUP_SCRIPTS[@]}"; do
-  echo ""
-  echo "▶️  Running setup script: $script"
-  
-  # Make script executable if not already
-  chmod +x "$script" 2>/dev/null || true
-  
-  # Run script
-  if bash "$script"; then
-    echo "✅ Setup script completed: $script"
-  else
-    echo "⚠️  Setup script failed: $script (exit code: $?)"
-    echo "Continuing anyway..."
-  fi
-done
-```
-
-### Step 7: Summary
-
-```bash
-echo ""
-echo "✅ Pull workflow completed"
-echo ""
-echo "Summary:"
-echo "  - Branch: $CURRENT_BRANCH"
-echo "  - Latest commit: $(git rev-parse HEAD)"
-echo "  - Setup scripts run: ${#SETUP_SCRIPTS[@]}"
-```
-
-### Step 8: Return to Original Directory (if in submodule mode)
-
-**Note**: If in submodule mode, we already returned to the parent directory in Step 6 to run setup scripts. This step is now a no-op, but kept for clarity.
-
-If submodule name was provided and we're not already in the parent directory:
-
-```bash
-if [ -n "$ORIGINAL_DIR" ] && [ "$(pwd)" != "$ORIGINAL_DIR" ]; then
-  cd "$ORIGINAL_DIR" || exit 1
-  echo "✅ Returned to main repository directory"
-fi
-```
-
-## Configuration
-
-Optional configuration in `foundation-config.yaml`:
-
-```yaml
-development:
-  pull:
-    auto_commit: true  # Automatically commit local changes before pull
-    conflict_strategy: "merge"  # "merge" | "rebase" | "abort"
-    run_setup_scripts: true  # Run setup scripts after pull
-    setup_scripts:
-      - "scripts/setup_agent_environment.sh"  # Custom list of scripts to run
-```
-
-## Error Handling
-
-- If commit fails: Abort and report error
-- If pull fails due to conflicts: List conflicts, pause for user resolution
-- If setup script fails: Log warning but continue (non-fatal)
-- If submodule not found: Exit with error
-
-## Inputs
-
-- `submodule_name` (optional string): Submodule name to scope operations to (e.g., "foundation")
-

package/.claude/skills/setup_symlinks.md

@@ -1,228 +0,0 @@
----
-name: setup_symlinks
-description: Setup Foundation Symlinks
----
-
-<!-- Source: foundation/agent_instructions/cursor_commands/setup_symlinks.md -->
-
-# 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 `.claude/rules/`
-2. Creates symlinks from `foundation/agent_instructions/cursor_commands/` to `.claude/skills/`
-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 `.claude/rules/` for foundation rule symlinks (using original filenames)
-- Check `.claude/skills/` 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 `.claude/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 `.claude/skills/`:**
-- `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
-

package/.codex/config.toml

@@ -1,92 +0,0 @@
-# Neotoma: no project overrides. Use user-level config for approval, sandbox, and behavior:
-#   ~/.codex/config.toml (macOS/Linux)
-# See: https://developers.openai.com/codex/config-basic
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"
-# --- end synced MCP servers ---
-
-# --- MCP servers synced from .cursor/mcp.json (do not edit by hand) ---
-[mcp_servers.web-scraper]
-command = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper/run-web-scraper-mcp.sh"
-cwd = "/Users/markmhendrickson/repos/neotoma/mcp/web-scraper"