Canonical turn protocol for agents writing to Neotoma. Bounded retrieval on the user message, store user message PART_OF conversation with REFERS_TO edges to retrieved entities, store assistant reply the same way. Use this skill in any agent loop that should persist conversation state to Neotoma.

2026-07-0327

end

markmhendrickson/neotoma

Session-end audit. Files remaining work as task entities and lists them as bullets, verifies all data intended for Neotoma storage from this session is actually stored, and persists what's missing. Invoke at the natural close of a working session, before context is lost.

2026-06-3027

status

markmhendrickson/neotoma

Mid-session status report. Summarizes what's been achieved so far this session and what work remains, in succinct qualitative prose and bullets with only light technical detail. Read-only — stores nothing, files nothing. Invoke any time to take stock without closing the session.

2026-06-3027

close-session

markmhendrickson/neotoma

Close a Neotoma working session — store the assistant reply and a session-close summary.

2026-06-2527

get-context

markmhendrickson/neotoma

Retrieve the bounded context for the current session — recent interactions and relevant entities.

2026-06-2527

start-session

markmhendrickson/neotoma

Begin a Neotoma working session — open a conversation and record the opening interaction.

2026-06-2527

name	setup_cursor_copies
description	Setup Foundation Cursor Copies

Setup Foundation Cursor Copies

Sets up foundation cursor rules and commands in .cursor/. When foundation is a git submodule, creates symlinks (stays in sync with git submodule update). Otherwise creates independent copies.

Command

setup_cursor_copies

setup cursor copies

Purpose

This command runs the foundation setup script (foundation/scriptsscripts/setup_claude_instructions.sh.sh) which:

If foundation is a git submodule: Delegates to setup_cursor_rules.sh and creates symlinks from foundation to .cursor/ (single source of truth; updates apply with git submodule update).
Otherwise: Creates independent copies of foundation rules/commands in .cursor/.
Uses original filenames (no prefix).
Removes existing foundation files before creating new ones.
Preserves any non-foundation 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

Submodule: Run after git submodule update (or any setup); symlinks keep .cursor/ in sync automatically.
Copy mode (foundation not a submodule): When you want independent copies, need to customize rules, symlinks are not suitable, or you version-control your own copies. Re-run after foundation updates to refresh.

Submodule vs copy behavior

When foundation is a git submodule (this command delegates to setup_cursor_rules):

Creates symlinks to foundation (single source of truth)
Updates automatically when foundation changes (git submodule update)
Cannot customize foundation rules without breaking the link

When foundation is a symlink or copy (this command uses copy mode):

Creates independent file copies
Uses original filenames (no prefix)
Does NOT update automatically when foundation changes
Can be customized per repository
Must re-run script to get foundation updates

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 Copy Script in Current Repository

Execute the script:

./foundation/scriptsscripts/setup_claude_instructions.sh.sh

Or if foundation is in parent directory:

../foundation/scriptsscripts/setup_claude_instructions.sh.sh

Step 3: Run Copy Script in Peer Repositories (If in Foundation Repo)

If running from the foundation repository itself (detected by presence of agent_instructions/cursor_skills/ directory):

Get current repository absolute path:
```
CURRENT_REPO=$(pwd -P)
```

Find peer repositories in parent directory:

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 copy script in peer repo using absolute path
      (cd "$peer_repo" && "$CURRENT_REPO/scriptsscripts/setup_claude_instructions.sh.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 copy script in each matching peer repo
Continues even if one peer repo fails

Expected output (when peer repos found):

[INFO] ✅ Cursor rules setup complete!
...
[INFO] Detected foundation repository - checking for peer repos...
[INFO] Found peer repo with foundation symlink: my-project
[INFO] Running copy setup script in my-project...
[INFO] Foundation is a git submodule; using symlinks (setup_cursor_rules)...  (or copy mode)
...
[INFO] ✅ Cursor rules setup complete!
[INFO] ✓ Successfully updated my-project

[INFO] Updated 1 peer repo(s)

Step 4: Verify Results

Check output:

Submodule: Script reports "Foundation is a git submodule; using symlinks", then rules linked. Check .claude/rules/ for symlinks; .cursor/skills/ is populated from foundation skills.
Copy mode: Script reports rules and skills copied. Check .claude/rules/ and .cursor/skills/ for regular files (not symlinks).

Expected output (submodule):

[INFO] Foundation is a git submodule; using symlinks (setup_cursor_rules)...
[INFO] Setting up cursor rules and commands...
[INFO] Creating symlinks for generic cursor rules...
  ✓ Linked security.mdc -> security.mdc
  ...
[INFO] ✅ Cursor rules setup complete!
[INFO]   Foundation rules linked: X
[INFO]   Foundation commands linked: Y

Expected output (copy mode):

[INFO] Setting up cursor rules and commands (copy mode)...
[INFO] Copying generic cursor rules...
  ✓ Copied security.mdc
  ...
[INFO] ✅ Cursor rules setup complete!
[INFO]   Rules copied: X
[INFO]   Commands copied: Y

What Gets Created

When foundation is a submodule (symlinks):

.claude/rules/ contains symlinks to foundation/agent_instructions/cursor_rules/. .cursor/skills/ is populated from foundation/agent_instructions/cursor_skills/ (skills replace legacy commands). Updates to foundation apply when you re-run setup.

When foundation is not a submodule (copies):

.claude/rules/ and .cursor/skills/ contain independent copies of foundation rules and skills (e.g. security.mdc, worktree_env.mdc, and full skill workflows). Re-run to refresh after foundation updates.

Note: Repository rules from docs/ are handled per setup_cursor_rules (symlinks when submodule) or copied in copy mode. Source files in docs/ remain the source of truth.

Behavior

Filenames:

Foundation rules/commands use original filenames (no prefix), e.g. security.mdc remains security.mdc.

Submodule (symlinks): Removes existing foundation files (symlinks or copies), then creates symlinks. Repo rules from docs/ are symlinked; any existing file at the target path (symlink or regular file) is removed and replaced with the symlink to the source.

Copy mode: Removes existing foundation files, then creates copies. Repo rules from docs/ are copied.

Existing Files: If a target already exists (symlink or regular file), it is removed and replaced with the symlink (or copy in copy mode). Source in docs/ or foundation is the single source of truth.

Existing Foundation Files: Removed first (prefixed and unprefixed), then new symlinks or copies created. Ensures output matches current foundation.

Copy mode only: Files are independent; foundation changes do not apply until you re-run. You can customize copies.

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 Skills Directory (optional)

Foundation workflows are in foundation/agent_instructions/cursor_skills/. If present, setup copies them to .cursor/skills/. If the directory is missing, setup still succeeds (rules only).

Notes

Submodule → symlinks: Foundation as git submodule yields symlinks; updates apply with git submodule update.
Otherwise → copies: Symlink or copy foundation yields independent copies; re-run to refresh.
Original filenames: Foundation rules/commands use original filenames (no prefix).
Repository rules: From docs/; symlinked or copied per mode. Source in docs/ remains source of truth.
When run from foundation repo: Propagates to peer repos in ../* that have foundation/ symlink to this repo.

setup-cursor-copies

Setup Foundation Cursor Copies

Command

Purpose

When to Use

Submodule vs copy behavior

Execution Instructions

Step 1: Verify Foundation Directory

Step 2: Run Copy Script in Current Repository

Step 3: Run Copy Script in Peer Repositories (If in Foundation Repo)

Step 4: Verify Results

What Gets Created

Behavior

Error Handling

Foundation Directory Not Found

Cursor Rules Directory Not Found

Cursor Skills Directory (optional)

Related Documents

Notes

Setup Foundation Cursor Copies

Command

Purpose

When to Use

Submodule vs copy behavior

Execution Instructions

Step 1: Verify Foundation Directory

Step 2: Run Copy Script in Current Repository

Step 3: Run Copy Script in Peer Repositories (If in Foundation Repo)

Step 4: Verify Results

What Gets Created

Behavior

Error Handling

Foundation Directory Not Found

Cursor Rules Directory Not Found

Cursor Skills Directory (optional)

Related Documents

Notes