@nemus-cli/nemus 0.2.1

package/skills/workspace-manager/references/generate-docs.md

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+# Generate Docs
+
+Generate workspace documentation including a README, dependency graph, and repository index.
+
+## Instructions
+
+```bash
+nemus generate-docs <workspace>
+```
+
+Alias:
+```bash
+w gd <workspace>
+```
+
+Without a workspace name, prompts interactively:
+```bash
+nemus generate-docs
+```
+
+## Generated Files
+
+Creates these files in the workspace root:
+- `WORKSPACE-README.md` — Overview of the workspace and its repos
+- `DEPENDENCY-GRAPH.md` — Mermaid diagram of inter-repo dependencies
+- `REPOSITORY-INDEX.md` — Detailed index of all repos
+
+## When to Suggest
+
+- After creating a workspace with many repos
+- When user wants to understand workspace structure
+- When onboarding someone to a multi-repo project
+
+## Success Criteria
+
+- All three documentation files are generated in the workspace directory.

package/skills/workspace-manager/references/ghq-status.md

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+# GHQ Status
+
+Check the status of ghq integration for faster repository cloning.
+
+## Instructions
+
+```bash
+nemus ghq-status
+```
+
+## What It Shows
+
+- Whether ghq is installed
+- ghq root directory and number of managed repos
+- How ghq accelerates workspace creation (cached local copies)
+
+## How ghq Works with Workspace Manager
+
+1. **First clone**: ghq downloads repo to its cache
+2. **Workspace creation**: Copies from ghq cache instead of cloning from remote
+3. **Subsequent clones**: Much faster (local copy vs network clone)
+4. **Isolation**: Each workspace still gets its own independent clone
+
+## When to Suggest
+
+- User reports slow workspace creation
+- User asks about optimizing clone performance
+- User asks what ghq is or whether to install it

package/skills/workspace-manager/references/go.md

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+# Go (Navigate to Workspace)
+
+Quickly navigate to a workspace directory. Works with the `nemgo` shell function for auto-CD.
+
+## Instructions
+
+With a known workspace name:
+```bash
+nemus go <name>
+```
+
+Without a name (interactive fuzzy picker):
+```bash
+nemus go
+```
+
+Or use the shell function (auto-CDs into the workspace):
+```bash
+nemgo <name>
+```
+
+The `nemgo` variant also launches Claude Code automatically if a session exists.
+
+## How It Works
+
+1. `nemus go` writes the workspace path to `~/.workspace-last-go`
+2. The shell integration function reads that file and runs `cd`
+3. If the workspace has an existing Claude session, it resumes it
+
+## Success Criteria
+
+- The terminal's working directory changes to the workspace path.
+- If a Claude session exists, it resumes automatically (with `nemgo`).

package/skills/workspace-manager/references/history.md

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+# History
+
+View operation history for workspace-manager commands.
+
+## Instructions
+
+### Show Recent History
+
+```bash
+nemus history
+nemus history show 50           # last 50 records
+nemus history show --command create   # filter by command
+nemus history show --workspace my-ws  # filter by workspace
+```
+
+### Show Statistics
+
+```bash
+nemus history stats
+```
+
+Shows total operations, success rate, average duration, and per-command usage counts.
+
+### Clear History
+
+```bash
+nemus history clear
+nemus history clear --yes    # skip confirmation
+```
+
+## Alias
+
+```bash
+w h              # same as nemus history
+w h stats        # same as nemus history stats
+```
+
+## Success Criteria
+
+- History records are displayed in a table with timestamp, command, workspace, duration, and status.
+- Stats show meaningful aggregations.

package/skills/workspace-manager/references/list-org-repos.md

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+# List Org Repos
+
+List all organization repositories from GitHub.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus cache list
+   ```
+   Pass `--force-refresh` (or `-f`) only if the user explicitly asks to refresh the cache:
+   ```bash
+   nemus cache list --force-refresh
+   ```
+
+2. Present the repos in a clear format. Since there may be many, consider:
+   - Grouping by prefix (api-, service-, lib-, etc.)
+   - Showing count totals
+   - Asking the user to narrow down with `nemus cache search <query>` if needed
+
+3. If the cache is stale, suggest `nemus cache refresh` to update it.
+
+## Success Criteria
+
+- All org repos are listed, optionally grouped by prefix.
+- User is guided toward `nemus cache search` if the list is too large to browse.

package/skills/workspace-manager/references/list-suites.md

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+# List Suites
+
+List all saved suites with their repo counts.
+
+## Instructions
+
+```bash
+nemus suite list
+```
+
+Present the suites showing name, number of repos, description (if available), and repo list.
+
+To create a workspace from a suite (non-interactive):
+```bash
+nemus suite use --suite <suite-name> --workspace <workspace-name> --yes
+```
+
+## Success Criteria
+
+- All available suites are listed with their repo counts and descriptions.
+- User is guided toward `nemus suite use` if they want to create a workspace from a suite.

package/skills/workspace-manager/references/list-workspaces.md

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+# List Workspaces
+
+List all existing workspaces managed by workspace-manager.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus list
+   ```
+   Pass `--archived` only if the user asks to see archived workspaces:
+   ```bash
+   nemus list --archived
+   ```
+
+2. Present the results showing:
+   - Workspace name
+   - Number of repositories
+   - Creation date
+   - Archived status (if applicable)
+
+3. If no workspaces exist, suggest creating one with `nemus create`.
+
+## Success Criteria
+
+- All active workspaces are listed with repo count and creation date.
+- Archived workspaces are shown only when explicitly requested.

package/skills/workspace-manager/references/mcp.md

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+# MCP Server
+
+Manage the MCP (Model Context Protocol) server integration with Claude Code.
+
+## Commands
+
+### Install
+
+Register the workspace-manager MCP server with Claude Code:
+```bash
+nemus mcp install
+```
+
+This also installs shell integration, permission sync hooks, and workspace skills.
+
+### Uninstall
+
+Remove the MCP server registration:
+```bash
+nemus mcp uninstall
+```
+
+### Upgrade
+
+Update hooks and skills without re-registering the MCP server:
+```bash
+nemus mcp upgrade
+```
+
+Use after updating the workspace-manager package.
+
+### Status
+
+Check if the MCP server is registered:
+```bash
+nemus mcp status
+```
+
+## What MCP Provides
+
+When installed, Claude Code gains access to workspace-manager tools:
+- `create-workspace`, `list-workspaces`, `workspace-status`, etc.
+- Enables natural language workspace management via `nemus -- <prompt>`
+
+## When to Suggest
+
+- After installing or upgrading workspace-manager
+- When Claude Code doesn't seem to have workspace tools
+- When `nemus -- <prompt>` fails to find MCP tools

package/skills/workspace-manager/references/remove-repo.md

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+# Remove Repo
+
+Remove a repository instance from a workspace.
+
+## Instructions
+
+1. Warn the user about any uncommitted changes before removing.
+
+2. Run the command:
+   ```bash
+   nemus remove-repo --workspace <name> --repos <dir-name> --yes
+   ```
+
+   Note: `--repos` takes the **directory name** inside the workspace (not the GitHub repo name — these differ when using suffixes).
+
+## Flags
+
+| Flag | Short | Description |
+|---|---|---|
+| `--workspace <name>` | `-w` | Target workspace |
+| `--repos <dir,...>` | `-r` | Comma-separated directory names to remove |
+| `--yes` | `-y` | Skip confirmation prompt |
+
+## Success Criteria
+
+- The specified repo directory is removed from the workspace after user confirmation.

package/skills/workspace-manager/references/run-command.md

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+# Run Command
+
+Run a shell command across all repositories in a workspace (3 concurrent, 5 minute timeout per repo).
+
+## Instructions
+
+```bash
+nemus run <workspace> <command>
+```
+
+Alias:
+```bash
+w r <workspace> <command>
+```
+
+Without a workspace name, prompts interactively:
+```bash
+nemus run "<command>"
+```
+
+## Examples
+
+```bash
+nemus run my-workspace "npm install"
+nemus run my-workspace "git status -s"
+nemus run my-workspace "npm test"
+nemus run my-workspace "echo hello"
+nemus run my-workspace "git checkout main"
+nemus run my-workspace "cat package.json | jq .version"
+```
+
+## Output
+
+Shows per-repo results:
+- ✓ for successful execution (with stdout)
+- ✗ for failed execution (with stderr)
+- Summary count of successes and failures
+
+Exits with code 1 if any repo failed.
+
+## Success Criteria
+
+- Command is executed in all repos and per-repo success/failure is reported.
+- stdout and stderr from each repo are clearly displayed.

package/skills/workspace-manager/references/search-repos.md

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+# Search Repos
+
+Search organization repositories by name or description using fuzzy matching.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus cache search <query>
+   ```
+
+2. Present matching repos with:
+   - Repository name
+   - Description
+   - URL
+
+3. If the user is looking for repos to add to a workspace, suggest:
+   - `nemus create` to create a new workspace with selected repos
+   - `nemus update` to add repos to an existing workspace
+
+## Success Criteria
+
+- Matching repos are listed with name, description, and URL.
+- Follow-up action (create or update workspace) is suggested if appropriate.

package/skills/workspace-manager/references/sessions.md

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+# Sessions
+
+Pick a workspace with an active Claude Code session and resume it.
+
+## Instructions
+
+Interactive only — displays a fuzzy-searchable list of workspaces with sessions:
+```bash
+nemus sessions
+```
+
+Alias:
+```bash
+w ses
+```
+
+## How It Works
+
+1. Scans for Claude Code sessions across all workspaces
+2. Shows them sorted by last active time
+3. User picks one → terminal CDs to that workspace and resumes the Claude session
+
+## When to Suggest
+
+- User asks to "continue where I left off"
+- User wants to resume work on a previous workspace
+- User asks about their recent Claude sessions

package/skills/workspace-manager/references/suite-create.md

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+# Suite Create
+
+Create a new suite (reusable collection of repositories) that can be used to quickly set up workspaces.
+
+## Instructions
+
+1. In interactive mode:
+   ```bash
+   nemus suite create
+   ```
+
+2. In non-interactive mode (for agents):
+   ```bash
+   nemus suite create --name <suite-name> --repos repo1,repo2,repo3 --description "optional description" --yes
+   ```
+
+3. After creation, confirm with the suite name and repo count.
+
+## Success Criteria
+
+- Suite is saved with the specified name and repos.
+- Suite appears in `nemus suite list`.

package/skills/workspace-manager/references/suite-delete.md

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+# Suite Delete
+
+Delete a saved suite.
+
+## Instructions
+
+1. In interactive mode:
+   ```bash
+   nemus suite delete
+   ```
+
+2. In non-interactive mode (for agents):
+   ```bash
+   nemus suite delete --name <suite-name> --yes
+   ```
+
+3. Confirm deletion.
+
+## Success Criteria
+
+- Suite is removed and no longer appears in `nemus suite list`.

package/skills/workspace-manager/references/suite-export.md

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+# Suite Export
+
+Export one or all suites to a JSON file for sharing.
+
+## Instructions
+
+1. Export all suites:
+   ```bash
+   nemus suite export ./suites.json
+   ```
+
+2. In interactive mode, you'll be prompted to choose a single suite or all.
+
+3. Share the exported file with teammates who can import it with `nemus suite import`.
+
+## Success Criteria
+
+- JSON file is created with suite data.
+- File can be imported with `nemus suite import`.

package/skills/workspace-manager/references/suite-import.md

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+# Suite Import
+
+Import suites from a JSON file (exported by `nemus suite export`).
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus suite import <file-path>
+   ```
+
+2. Existing suites with the same name will be skipped by default.
+
+3. After import, verify with `nemus suite list`.
+
+## Success Criteria
+
+- Suites from the file are imported.
+- Imported suites appear in `nemus suite list`.

package/skills/workspace-manager/references/suite-use.md

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+# Suite Use
+
+Create a new workspace from a saved suite.
+
+## Instructions
+
+1. In interactive mode:
+   ```bash
+   nemus suite use
+   ```
+
+2. In non-interactive mode (for agents):
+   ```bash
+   nemus suite use --suite <suite-name> --workspace <workspace-name> --yes
+   ```
+
+3. This will:
+   - Clone all repos defined in the suite
+   - Run any post-clone hooks configured in the suite
+   - Set up Claude Code integration
+
+4. After creation, suggest `nemus status <workspace>` to verify.
+
+## Success Criteria
+
+- Workspace is created with all suite repos cloned.
+- Post-clone hooks (if any) are executed.

package/skills/workspace-manager/references/switch-branch.md

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+# Switch Branch
+
+Switch all repositories in a workspace to a specified branch.
+
+## Instructions
+
+```bash
+nemus branch switch --workspace <name> --branch <branch-name>
+```
+
+## Flags
+
+| Flag | Short | Description |
+|---|---|---|
+| `--workspace <name>` | `-w` | Target workspace |
+| `--branch <name>` | `-b` | Target branch name |
+
+If some repos fail to switch (due to uncommitted changes), suggest:
+- Committing or stashing changes first
+- Using `nemus status <name>` to check the state
+
+## Success Criteria
+
+- All repos without uncommitted changes are switched to the target branch.
+- Repos that failed to switch are clearly reported with the reason.

package/skills/workspace-manager/references/update-cache.md

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+# Update Cache
+
+Force refresh the GitHub repository cache so newly added repos become searchable.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus cache refresh
+   ```
+   Or use the short flag on any command:
+   ```bash
+   nemus cache list --force-refresh
+   ```
+
+2. Report the result (number of repos cached, etc.).
+
+3. Suggest using `nemus cache search <query>` or `nemus cache list` to browse the updated list.
+
+## Success Criteria
+
+- Cache is refreshed and the updated repo count is reported.

package/skills/workspace-manager/references/update-workspace.md

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+# Update Workspace
+
+Add more repositories to an existing workspace.
+
+## Instructions
+
+1. Run the command with flags (non-interactive):
+   ```bash
+   nemus update --workspace <name> --repos <r1,r2,...>
+   ```
+
+   Or interactively:
+   ```bash
+   nemus update
+   ```
+
+2. Report which repos were added successfully and which were skipped (already exist).
+
+## Flags
+
+| Flag | Short | Description |
+|---|---|---|
+| `--workspace <name>` | `-w` | Target workspace |
+| `--repos <r1,r2,...>` | `-r` | Comma-separated repo names to add. Use `repo:suffix` to add the same repo again under a separate folder. |
+
+## Adding the same repo more than once (instances)
+
+The same repository can live in a workspace multiple times under different
+folders — useful for comparing branches/versions side by side, or keeping a
+second checkout instead of a `git worktree` (which `nemus status`/`nemus sync` do NOT
+track). Append `:suffix` to the repo name; the repo is cloned into
+`<repo>-<suffix>`:
+
+```bash
+# casper already in the workspace — add a second checkout for branch CAS-101
+nemus update --workspace my-ws --repos casper:cas-101    # -> folder casper-cas-101
+```
+
+The suffix may contain letters, numbers, hyphens, and underscores. Each
+instance is tracked independently by `nemus status` and `nemus sync` and is labeled
+`(instance: <folder>)` in the workspace context file.
+
+> Do NOT use `git worktree` inside a workspace to get a second checkout of a
+> tracked repo — worktrees are invisible to `nemus status`/`nemus sync`. Use
+> `nemus update --repos <repo>:<suffix>` instead.
+
+## Success Criteria
+
+- All specified repos are cloned into the workspace.
+- User is informed of any repos skipped due to already existing.

package/skills/workspace-manager/references/workspace-cleanup.md

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+# Workspace Cleanup
+
+Remove node_modules and build artifacts from all repos in a workspace to free disk space.
+
+## Instructions
+
+```bash
+nemus cleanup <workspace> --all --yes
+```
+
+Or specify what to clean:
+```bash
+nemus cleanup <workspace> --node-modules --yes
+nemus cleanup <workspace> --build --yes
+nemus cleanup <workspace> --git-clean --yes
+```
+
+## Flags
+
+| Flag | Description |
+|---|---|
+| `--all` | Remove everything (node_modules + build artifacts + git clean) |
+| `--node-modules` | Remove `node_modules` directories |
+| `--build` | Remove `dist`, `build`, `.next`, `coverage`, `out` |
+| `--git-clean` | Remove untracked files via git clean |
+| `--yes` / `-y` | Skip confirmation prompt |
+
+Remind the user they'll need to run `npm install` before building again.
+
+## Success Criteria
+
+- Selected directories are removed and disk space freed is reported.
+- User is reminded to re-run `npm install` before building.

package/skills/workspace-manager/references/workspace-diff.md

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+# Workspace Diff
+
+Show diff summary (staged/unstaged file counts, insertions, deletions) for all repos in a workspace.
+
+## Instructions
+
+1. If no workspace is specified, run `nemus list` and ask which one.
+
+2. Run:
+   ```bash
+   nemus diff
+   ```
+   Or target a specific workspace:
+   ```bash
+   nemus diff <name>
+   ```
+
+3. Present a clear summary showing per-repo:
+   - Number of staged/unstaged files
+   - Lines inserted/deleted
+   - Which files changed
+
+4. If the user wants full diff content, they can pipe through `less` or redirect to a file.
+
+## Success Criteria
+
+- Per-repo diff summary is presented with file counts and line statistics.