@nemus-cli/nemus 0.2.1

package/skills/create-workspace.md

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+---
+name: create-workspace
+description: Create a new multi-repo workspace by cloning repositories from the org using `nemus create`. ALWAYS use this skill — never run `git clone` directly — when the user asks to create a workspace, set up a new workspace, or start fresh with a set of repos.
+---
+
+# Create Workspace
+
+Create a new workspace by cloning repositories.
+
+## Resolving Repositories
+
+If the user hasn't specified which repos to clone, help them discover:
+```bash
+nemus cache search <keyword>
+```
+
+## Creating the Workspace
+
+Run non-interactively:
+```bash
+nemus create --workspace <name> --repos <repo1,repo2,...> --yes
+```
+
+Or interactively (prompts for workspace name and repos):
+```bash
+nemus create
+```
+
+## Presenting Results
+
+Report:
+- Workspace created at path
+- Successfully cloned repos
+- Any failures with their error reason
+
+## Suggested Follow-ups
+
+- `nemus status <name>` to verify
+- `nemus update --workspace <name> --repos <more-repos>` to add more repos later

package/skills/delete-workspace.md

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+---
+name: delete-workspace
+description: Delete one or more workspaces and all their contents permanently
+---
+
+# Delete Workspace
+
+Delete one or more workspaces permanently.
+
+## Resolving the Workspace
+
+If the user hasn't specified which workspace to delete:
+```bash
+nemus list 2>&1 | cat
+```
+
+## Deleting
+
+Run non-interactively:
+```bash
+nemus delete --workspace <name> --yes
+```
+
+Or interactively (prompts for confirmation):
+```bash
+nemus delete
+```
+
+## Important Notes
+
+- This permanently removes the workspace directory and all its contents
+- There is no undo — repos will need to be re-cloned
+- Always confirm with the user before deleting
+
+## Suggested Follow-ups
+
+- `nemus list` to verify the workspace is gone

package/skills/list-org-repos.md

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+---
+name: list-org-repos
+description: List all organization repositories from GitHub
+---
+
+# List Org Repos
+
+List all repositories in the GitHub organization.
+
+## Running
+
+```bash
+nemus cache list
+```
+
+If the cache is empty or stale:
+```bash
+nemus cache refresh
+```
+
+## Presenting Results
+
+Show repo names. Can be filtered by searching:
+```bash
+nemus cache search <keyword>
+```

package/skills/list-suites.md

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+---
+name: list-suites
+description: List all saved suites (reusable repo collections)
+---
+
+# List Suites
+
+List all saved suites (reusable collections of repos).
+
+## Running
+
+```bash
+nemus suite list
+```
+
+## Presenting Results
+
+Show each suite's name and the repos it contains.
+
+## Related
+
+- `nemus suite create` to create a new suite
+- `nemus suite use` to create a workspace from a suite
+- `nemus suite delete` to remove a suite

package/skills/list-workspaces.md

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+---
+name: list-workspaces
+description: List all workspaces with their repo counts and creation dates
+---
+
+# List Workspaces
+
+List all workspaces with their status.
+
+## Listing
+
+```bash
+nemus list
+```
+
+Note: This command opens an interactive picker. To just see the output without selecting, pipe it:
+```bash
+nemus list 2>&1 | cat
+```
+
+## Presenting Results
+
+Show each workspace with:
+- Name
+- Number of repositories
+- Creation date
+- Last active session (if any)

package/skills/refresh-workspace-docs.md

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+---
+name: refresh-workspace-docs
+description: Refresh the per-repo documentation embedded in a workspace's context file (AGENTS.md / .claude.md). Use when a workspace was created a while ago and its repos have since received updates to their README, AGENTS.md, or CLAUDE.md files, so the embedded copies in the workspace context are stale.
+---
+
+# Refresh Workspace Docs
+
+When a workspace is created, each repo's own `AGENTS.md` / `CLAUDE.md` is
+embedded into the workspace-level context file (`AGENTS.md` / `.claude.md`)
+under the **Per-Repository Context** section. Those embedded copies are a
+snapshot taken at creation time — they do **not** auto-update when the repo
+later receives new commits that change its README or agent docs.
+
+This skill refreshes that embedded content so the agent works from the
+latest per-repo guidance.
+
+## When to Use
+
+- A workspace was created days/weeks ago and the repos have since changed.
+- A repo's `AGENTS.md` / `CLAUDE.md` / `README.md` was updated upstream and
+  you want the workspace context to reflect it.
+- The agent seems to be following outdated repo-specific instructions.
+- After a teammate merges changes to a repo's documentation.
+
+## Workflow
+
+Two steps: **sync the repos to latest**, then **regenerate the context**.
+
+### 1. Pull the latest for every repo in the workspace
+
+```bash
+nemus sync <workspace-name>
+```
+
+This `git pull`s every repo so their on-disk `README.md`, `AGENTS.md`, and
+`CLAUDE.md` reflect the latest upstream content. (Omit the name to sync the
+current workspace.)
+
+### 2. Regenerate the workspace context
+
+```bash
+w migrate
+```
+
+`nemus migrate` re-reads each repo's context files from disk and **surgically
+updates only the `## Per-Repository Context` section** of the workspace
+`AGENTS.md` / `.claude.md`. Your own notes (the `## Notes` section, saved
+`CONTEXT.md`, etc.) are preserved untouched.
+
+Preview what would change first with:
+
+```bash
+w migrate --dry-run
+```
+
+## What Gets Refreshed
+
+The `## Per-Repository Context` section is rebuilt from each repo's context
+file, discovered in this priority order (per repo, up to 2 directory levels
+deep for monorepo packages):
+
+1. `AGENTS.md`
+2. `.claude.md`
+3. `CLAUDE.md`
+
+Each repo's content is embedded with imperative scoping ("You MUST follow
+these rules whenever you work with files inside `<repo>/`") and placed near
+the top of the workspace context file so the agent weights it heavily.
+
+## Notes
+
+- This only refreshes **embedded** per-repo docs in the workspace context
+  file. The repos themselves are updated by `nemus sync` in step 1.
+- `nemus migrate` runs across **all** workspaces. That's safe and idempotent —
+  every workspace gets its per-repo section refreshed from current on-disk
+  content. Use `--dry-run` first if you want to see scope.
+- If a workspace has no repo-level context files, the section is omitted
+  (or removed if it previously existed).
+
+## Example
+
+```bash
+# Workspace 'payments' was created 3 weeks ago; partnerships-api has since
+# rewritten its AGENTS.md with new Jira board instructions.
+
+nemus sync payments        # pull latest — partnerships-api/AGENTS.md now current
+w migrate --dry-run    # preview: "payments: would embed per-repo context from 4 location(s)"
+w migrate              # apply — workspace AGENTS.md now has the new instructions
+```

package/skills/remove-repo.md

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+---
+name: remove-repo
+description: Remove a repository from a workspace
+---
+
+# Remove Repo
+
+Remove a repository from a workspace.
+
+## Running
+
+```bash
+nemus remove-repo --workspace <name> --repo <repo-name> --yes
+```
+
+Or interactively:
+```bash
+nemus remove-repo
+```
+
+## Important Notes
+
+- This removes the repo directory from the workspace
+- The repo is not deleted from GitHub, only removed locally
+- The workspace metadata is updated to reflect the removal

package/skills/run-command.md

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+---
+name: run-command
+description: Run a shell command across all repos in a workspace
+---
+
+# Run Command
+
+Run a shell command across all repos in a workspace.
+
+## Running
+
+```bash
+nemus run <workspace-name> "<command>"
+```
+
+Example:
+```bash
+nemus run my-workspace "git log --oneline -5"
+```
+
+## Presenting Results
+
+Report the output from each repo, clearly labeling which output comes from which repo.

package/skills/save-context.md

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+---
+name: save-context
+description: Save progress summary to workspace (persists across /clear and session restarts). Use when you want to preserve important context, findings, or progress before clearing conversation history.
+---
+
+# Save Context
+
+Save a progress summary or important context to the workspace. This persists in `CONTEXT.md` and survives `/clear`, session restarts, and agent switches.
+
+## When to Use
+
+- Before `/clear` to preserve progress
+- After completing a significant milestone
+- To leave notes for the next session
+- When switching between tasks in the same workspace
+
+## Using the MCP Tool (Claude Code)
+
+Call `mcp__workspace-manager__save-context` with:
+- `workspace` (string): the workspace name
+- `content` (string): markdown content to save
+- `append` (boolean, optional): true to append, false to replace (default: false)
+
+## Using the CLI (any agent)
+
+```bash
+# Replace existing context
+nemus save-context -m "Completed auth refactor. Next: update payment service endpoints."
+
+# Append to existing context
+nemus save-context --append -m "Fixed CI failures. All tests passing."
+
+# From a file
+nemus save-context -f progress-notes.md
+
+# Pipe content
+echo "summary here" | nemus save-context
+```
+
+## What to Save
+
+Good context summaries include:
+- **What was done** — completed tasks, merged PRs
+- **Current state** — what's working, what's broken
+- **Next steps** — what to do next
+- **Key decisions** — architectural choices made and why
+- **Blockers** — what's blocking progress
+
+## Example
+
+```markdown
+## Progress
+
+- Refactored auth service to use JWT tokens (PR #42 merged)
+- Updated partnerships-api to call new auth endpoints
+- Fixed rate limiting bug in payment-gateway
+
+## Current State
+
+All services passing CI. Auth migration is complete for internal services.
+External API consumers still use legacy tokens (tracked in JIRA PAY-123).
+
+## Next Steps
+
+1. Migrate external consumers to JWT (need coordination with partners team)
+2. Add monitoring dashboard for token refresh failures
+3. Remove legacy token support after 30-day deprecation window
+```

package/skills/search-repos.md

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+---
+name: search-repos
+description: Search org repositories by name or description
+---
+
+# Search Repos
+
+Search for repositories in the GitHub organization.
+
+## Searching
+
+```bash
+nemus cache search <keyword>
+```
+
+This searches the cached list of org repos by name. Results show repo name and description.
+
+## If Cache is Empty
+
+```bash
+nemus cache refresh
+```
+
+Then search again.
+
+## Presenting Results
+
+Show matching repos with their names and descriptions. If the user wants to add repos to a workspace, suggest:
+```bash
+nemus update --workspace <name> --repos <repo1,repo2> --yes
+```

package/skills/snapshot-list.md

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+---
+name: snapshot-list
+description: List all saved workspace snapshots
+---
+
+# Snapshot List
+
+List all saved workspace snapshots.
+
+## Running
+
+```bash
+nemus history
+```
+
+## Presenting Results
+
+Show snapshot entries with timestamps and operation types.

package/skills/snapshot-save.md

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+---
+name: snapshot-save
+description: Save a snapshot of the current workspace state
+---
+
+# Snapshot Save
+
+Snapshots are automatically saved by workspace-manager operations (create, update, delete, etc.). There is no separate snapshot command — the history command shows past operations:
+
+```bash
+nemus history
+```

package/skills/switch-branch.md

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+---
+name: switch-branch
+description: Switch all repos in a workspace to a specified branch
+---
+
+# Switch Branch
+
+Switch all repos in a workspace to a specified branch.
+
+## Running
+
+```bash
+nemus branch switch <workspace-name> <branch-name>
+```
+
+## Presenting Results
+
+Report which repos were switched and any that couldn't switch (e.g., uncommitted changes).

package/skills/update-cache.md

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+---
+name: update-cache
+description: Force refresh the GitHub repository cache
+---
+
+# Update Cache
+
+Force refresh the GitHub repository cache.
+
+## Running
+
+```bash
+nemus cache refresh
+```
+
+This fetches the latest list of repositories from the GitHub org and updates the local cache.
+
+## When to Use
+
+- When `nemus cache search` doesn't find a recently created repo
+- Periodically to keep the cache fresh (auto-refreshes daily)

package/skills/update-workspace.md

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+---
+name: update-workspace
+description: Add one or more repositories to an existing workspace. ALWAYS use this skill — never run `git clone` directly — when the user asks to add, clone, include, or pull a new repo into the current workspace. Triggers on phrases like "add repo X", "include X in this workspace", "I need X here", "clone X into workspace", "add a service".
+---
+
+# Update Workspace
+
+> **CRITICAL**: NEVER use `git clone` directly to add repositories to a workspace.
+> Always use `nemus update` — it registers the repo in workspace metadata, updates
+> the context file, and keeps `nemus status`/`nemus sync` working correctly.
+
+Add more repositories to an existing workspace.
+
+## Resolving the Workspace
+
+If the user hasn't specified a workspace, run:
+```bash
+nemus list 2>&1 | cat
+```
+
+Or to see what's in a specific workspace (from inside the workspace directory):
+```bash
+cat .workspace-meta.json
+```
+
+## Resolving Repositories
+
+If the user hasn't specified which repos to add, help them discover:
+```bash
+nemus cache search <keyword>
+```
+
+To see what's already in the workspace (avoid adding duplicates):
+```bash
+cat .workspace-meta.json | jq '.repositories[].name'
+```
+
+## Adding Repos
+
+Run the update command non-interactively:
+```bash
+nemus update --workspace <name> --repos <repo1,repo2,...> --yes
+```
+
+### Adding the same repo more than once (instances)
+
+Append `:suffix` to a repo name to add it again under a separate folder
+(`<repo>-<suffix>`) — e.g. a second checkout for another branch instead of a
+`git worktree` (worktrees are invisible to `nemus status`/`nemus sync`):
+```bash
+nemus update --workspace <name> --repos casper:cas-101 --yes   # -> casper-cas-101
+```
+Suffix = letters, numbers, hyphens, underscores. Each instance is tracked
+independently by `nemus status`/`nemus sync`.
+
+## Presenting Results
+
+The command output shows which repos were added and which were skipped. Report:
+- Successfully added repos
+- Skipped repos (already exist in workspace) - this is not an error
+- Any failures with their error reason
+
+## Suggested Follow-ups
+
+- `nemus status <workspace>` to verify the new repos
+- `nemus sync <workspace>` to pull latest on all repos

package/skills/workspace-cleanup.md

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+---
+name: workspace-cleanup
+description: Remove node_modules and build artifacts to free disk space
+---
+
+# Workspace Cleanup
+
+Remove node_modules and build artifacts to free disk space.
+
+## Running
+
+```bash
+nemus cleanup <workspace-name>
+```
+
+## Presenting Results
+
+Report how much disk space was freed and which directories were removed.

package/skills/workspace-diff.md

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+---
+name: workspace-diff
+description: Show diff summary for all repos in a workspace
+---
+
+# Workspace Diff
+
+Show diff summary across all repos in a workspace.
+
+## Running
+
+```bash
+nemus diff <workspace-name>
+```
+
+Or for the current workspace:
+```bash
+nemus diff
+```
+
+## Presenting Results
+
+Report per-repo diff stats (files changed, insertions, deletions).

package/skills/workspace-doctor.md

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+---
+name: workspace-doctor
+description: Run health checks on a workspace
+---
+
+# Workspace Doctor
+
+Run health checks on a workspace.
+
+## Running
+
+```bash
+nemus doctor <workspace-name>
+```
+
+Or for the current workspace:
+```bash
+nemus doctor
+```
+
+## Presenting Results
+
+Report any issues found (missing repos, broken git state, etc.) and suggestions for fixes.

package/skills/workspace-info.md

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+---
+name: workspace-info
+description: Get detailed metadata for a workspace
+---
+
+# Workspace Info
+
+Get detailed metadata for a workspace including all repository info, tags, and disk path.
+
+## Resolving the Workspace
+
+If the user hasn't specified a workspace name, list them:
+```bash
+nemus list 2>&1 | cat
+```
+
+## Getting Info
+
+Read the workspace metadata file (path is relative to the workspace directory):
+```bash
+cat <workspace-path>/.workspace-meta.json
+```
+
+The workspace path can be found by checking the current directory or using:
+```bash
+nemus status <workspace-name>
+```
+
+## Presenting Results
+
+The JSON contains workspace metadata. Present clearly:
+
+- **Name** and **creation date**
+- **Disk path** where the workspace lives
+- **Repositories** - list each with:
+  - Directory name (may differ from repo name if a suffix was used)
+  - Clone URL
+  - Status (success/failed from creation)
+- **Tags** and any custom metadata if present
+
+## Suggested Follow-ups
+
+- `nemus status <workspace>` to see current git status of each repo
+- `nemus update --workspace <name> --repos <repos>` to add more repos
+- `nemus doctor <workspace>` to check workspace health