@nemus-cli/nemus 0.2.1

package/skills/workspace-manager/SKILL.md

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+---
+name: workspace-manager
+description: Manage multi-repo development workspaces — create, sync, branch, diff, clone, archive, analyze dependencies, run commands across repos, check status, clean up, delete, list org repos, search repos, list suites, remove repo, cache, suite management, sessions, history, generate docs, configure, MCP server, AI prompt. Use when working with workspaces, repos, branches, git operations across multiple repos, or the `nemus` CLI tool. NEVER use `git clone` directly — always use `nemus update` to add repos and `nemus create` to create workspaces.
+bashPattern: "\\bnemus\\s+(create|list|update|delete|sync|status|diff|run|go|doctor|analyze-deps|history|cleanup|remove-repo|archive|sessions|generate-docs|configure|configure-claude|ghq-status|tui|dashboard|dash|branch|suite|cache|mcp|--)\\b"
+---
+
+# Workspace Manager
+
+> **CRITICAL — Read before taking any action:**
+> - **NEVER** run `git clone` directly to add a repository to a workspace.
+> - **NEVER** run `git clone` directly to create a workspace.
+> - **NEVER** use `git worktree` to get a second checkout of a tracked repo — worktrees are invisible to `nemus status`/`nemus sync`. Add another instance with `nemus update --repos <repo>:<suffix>` instead.
+> - **ONLY read code from repos in the CURRENT workspace.** If you need to read or reference code from a repo that isn't in the current workspace, add it with `nemus update --workspace <current> --repos <repo> --yes` and read it there. **NEVER** read that repo's code from another workspace, a global ghq/clone path, or anywhere outside the current workspace — other workspaces may be on different branches or stale, and reading them silently breaks context isolation.
+> - **ALWAYS** use `nemus update --workspace <name> --repos <repo> --yes` to add repos.
+> - To add the **same repo more than once** (e.g. a second branch checkout), use `nemus update --workspace <name> --repos <repo>:<suffix> --yes` — it clones into `<repo>-<suffix>` and is tracked independently.
+> - **ALWAYS** use `nemus create --workspace <name> --repos <repos> --yes` to create workspaces.
+> - Direct git operations bypass workspace metadata, break `nemus status`/`nemus sync`, and leave context files stale.
+
+Manage multi-repo development workspaces using the `nemus` CLI tool (alias: `nem`).
+
+All commands support `--help` for detailed usage. The CLI uses Commander.js — every command has auto-generated help at root, command, and subcommand levels.
+
+## Global Flags
+
+These flags work on any command:
+
+| Flag | Short | Description |
+|---|---|---|
+| `--force-refresh` | `-f` | Force refresh GitHub repos (skip cache) |
+| `--yes` | `-y` | Skip all confirmation prompts |
+| `--version` | `-V` | Print version number |
+| `--help` | `-h` | Show help for any command |
+
+## Non-Interactive Usage (for agents/scripts)
+
+Every command can be run fully non-interactively by providing all required options as flags. When a required value (like workspace name) is missing and there's no TTY, the command will error with a usage hint.
+
+Pattern: **options-first with interactive fallback**.
+- If a flag is provided, it's used directly.
+- If a flag is omitted and a TTY is available, Inquirer prompts the user.
+- `--yes` / `-y` skips all confirmation prompts, and — for commands that create a workspace (`create`, `suite use`) — also skips auto-launching the AI agent afterward in the shell integration, so the command returns immediately instead of dropping into an interactive `claude`/`pi`/`opencode` session.
+
+```bash
+# Fully non-interactive
+nemus create --workspace payments --repos partnerships-api,payments-db --yes
+
+# Partially interactive (prompts for repos)
+nemus create --workspace payments
+
+# Fully interactive (prompts for everything)
+nemus create
+```
+
+## Command Aliases
+
+| Command | Alias(es) | Command | Alias(es) |
+|---------|-----------|---------|-----------|
+| `create` | `c` | `diff` | `di` |
+| `list` | `l` | `run` | `r` |
+| `update` | `u` | `archive` | `a` |
+| `delete` | `d`, `del` | `sessions` | `ses` |
+| `sync` | `s` | `cleanup` | `cl` |
+| `status` | `st` | `remove-repo` | `rr` |
+| `doctor` | `doc` | `generate-docs` | `gd` |
+| `analyze-deps` | `ad` | `configure` | `cfg` |
+| `history` | `h` | `configure-claude` | `cc` |
+| `dashboard` | `dash` | | |
+
+## Quick Start
+
+| What you want to do | Reference | CLI Command |
+|---|---|---|
+| Create a workspace | [create-workspace](references/create-workspace.md) | `nemus create` |
+| Add repos to workspace | [update-workspace](references/update-workspace.md) | `nemus update` |
+| Check git status | [workspace-status](references/workspace-status.md) | `nemus status <name>` |
+| Pull latest changes | [workspace-sync](references/workspace-sync.md) | `nemus sync <name>` |
+| List all workspaces | [list-workspaces](references/list-workspaces.md) | `nemus list` |
+| Navigate to workspace | [go](references/go.md) | `nemus go <name>` or `nemgo <name>` |
+| Search for repos | [search-repos](references/search-repos.md) | `nemus cache search <query>` |
+| Resume Claude session | [sessions](references/sessions.md) | `nemus sessions` |
+
+## Command Reference
+
+### Core Workspace Lifecycle
+
+| Intent | Reference | CLI | Alias |
+|---|---|---|---|
+| Create new workspace | [create-workspace](references/create-workspace.md) | `nemus create` | `c` |
+| Add repos to workspace | [update-workspace](references/update-workspace.md) | `nemus update` | `u` |
+| Delete workspace permanently | [delete-workspace](references/delete-workspace.md) | `nemus delete` | `d` |
+| Archive / unarchive workspace | [archive-workspace](references/archive-workspace.md) | `nemus archive` | `a` |
+| List all workspaces | [list-workspaces](references/list-workspaces.md) | `nemus list` | `l` |
+| Navigate to workspace | [go](references/go.md) | `nemus go [name]` | — |
+
+### Status & Operations
+
+| Intent | Reference | CLI | Alias |
+|---|---|---|---|
+| Git status across repos | [workspace-status](references/workspace-status.md) | `nemus status [name]` | `st` |
+| Pull latest (git sync) | [workspace-sync](references/workspace-sync.md) | `nemus sync [name]` | `s` |
+| Show diff summary | [workspace-diff](references/workspace-diff.md) | `nemus diff [name]` | `di` |
+| Run shell command across repos | [run-command](references/run-command.md) | `nemus run [name] <cmd>` | `r` |
+| Health check | [workspace-doctor](references/workspace-doctor.md) | `nemus doctor [name]` | `doc` |
+| Clean node_modules / artifacts | [workspace-cleanup](references/workspace-cleanup.md) | `nemus cleanup <name>` | `cl` |
+| Remove repo from workspace | [remove-repo](references/remove-repo.md) | `nemus remove-repo` | `rr` |
+| Analyze inter-repo deps | [analyze-deps](references/analyze-deps.md) | `nemus analyze-deps [name]` | `ad` |
+| Generate docs for workspace | [generate-docs](references/generate-docs.md) | `nemus generate-docs [name]` | `gd` |
+
+### Branch Management
+
+| Intent | Reference | CLI |
+|---|---|---|
+| Switch branch across repos | [switch-branch](references/switch-branch.md) | `nemus branch switch` |
+| Create branch across repos | [branch-create](references/branch-create.md) | `nemus branch create` |
+| Merge branches across repos | [branch-merge](references/branch-merge.md) | `nemus branch merge <ws> <src> <tgt>` |
+| Rebase branches across repos | [branch-rebase](references/branch-rebase.md) | `nemus branch rebase <ws> <base>` |
+
+### Suites (Reusable Repo Collections)
+
+| Intent | Reference | CLI |
+|---|---|---|
+| List saved suites | [list-suites](references/list-suites.md) | `nemus suite list` |
+| Create a suite | [suite-create](references/suite-create.md) | `nemus suite create` |
+| Delete a suite | [suite-delete](references/suite-delete.md) | `nemus suite delete` |
+| Export suite(s) to JSON | [suite-export](references/suite-export.md) | `nemus suite export [file]` |
+| Import suite(s) from JSON | [suite-import](references/suite-import.md) | `nemus suite import <file>` |
+| Create workspace from suite | [suite-use](references/suite-use.md) | `nemus suite use` |
+
+### Cache & Repo Discovery
+
+| Intent | Reference | CLI |
+|---|---|---|
+| Search org repos | [search-repos](references/search-repos.md) | `nemus cache search <query>` |
+| List all org repos | [list-org-repos](references/list-org-repos.md) | `nemus cache list` |
+| View cache statistics | [cache-info](references/cache-info.md) | `nemus cache info` |
+| Refresh repo cache | [update-cache](references/update-cache.md) | `nemus cache refresh` |
+| Clear cache | [cache-clear](references/cache-clear.md) | `nemus cache clear` |
+
+### Sessions & History
+
+| Intent | Reference | CLI | Alias |
+|---|---|---|---|
+| Resume Claude session | [sessions](references/sessions.md) | `nemus sessions` | `ses` |
+| Agent management dashboard | [dashboard](references/dashboard.md) | `nemus dashboard` | `dash` |
+| View operation history | [history](references/history.md) | `nemus history` | `h` |
+| View history statistics | [history](references/history.md) | `nemus history stats` | — |
+| Clear history | [history](references/history.md) | `nemus history clear` | — |
+
+### Configuration
+
+| Intent | Reference | CLI | Alias |
+|---|---|---|---|
+| Configure workspace manager | [configure](references/configure.md) | `nemus configure` | `cfg` |
+| Configure Claude integration | [configure-claude](references/configure-claude.md) | `nemus configure-claude` | `cc` |
+| Check ghq status | [ghq-status](references/ghq-status.md) | `nemus ghq-status` | — |
+
+### MCP Server
+
+| Intent | Reference | CLI |
+|---|---|---|
+| Install MCP server | [mcp](references/mcp.md) | `nemus mcp install` |
+| Uninstall MCP server | [mcp](references/mcp.md) | `nemus mcp uninstall` |
+| Upgrade MCP hooks/skills | [mcp](references/mcp.md) | `nemus mcp upgrade` |
+| Check MCP status | [mcp](references/mcp.md) | `nemus mcp status` |
+
+### AI Assistant
+
+| Intent | Reference | CLI |
+|---|---|---|
+| Natural language workspace management | [ai-prompt](references/ai-prompt.md) | `nemus -- <prompt>` |
+
+### Interactive TUI
+
+| Intent | CLI |
+|---|---|
+| Launch full interactive terminal UI | `nemus tui` |
+
+## Routing
+
+When the user's intent matches a row above, read the corresponding reference file for step-by-step instructions before running any CLI command. If no reference file exists for a command, use `nemus <command> --help` to get usage details.
+
+> **Reminder**: Do not use bare `git clone`, `git pull`, or other git commands to manage workspace repos.
+> All repo management **must** go through `nemus` commands so that workspace metadata and context files stay in sync.
+
+## Deprecated Aliases
+
+These still work but print a deprecation warning. Use the modern form instead:
+
+| Old | New |
+|-----|-----|
+| `nemus sc` | `nemus suite create` |
+| `nemus sls` | `nemus suite list` |
+| `nemus sd` | `nemus suite delete` |
+| `nemus se` | `nemus suite export` |
+| `nemus si` | `nemus suite import` |
+| `nemus fs` | `nemus suite use` |
+| `nemus sb` | `nemus branch switch` |
+| `nemus bc` | `nemus branch create` |
+| `nemus bm` | `nemus branch merge` |
+| `nemus br` | `nemus branch rebase` |
+| `nemus uc` | `nemus cache refresh` |

package/skills/workspace-manager/references/ai-prompt.md

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+# AI Prompt
+
+Use natural language to manage workspaces via Claude Code with MCP tools.
+
+## Instructions
+
+```bash
+nemus -- <prompt>
+```
+
+The `--` separates the workspace command from the natural language prompt.
+
+## Examples
+
+```bash
+nemus -- "Create a workspace with all payments repos"
+nemus -- "What workspaces do I have?"
+nemus -- "Add payments-db to my payments workspace"
+nemus -- "Show me the status of my platform workspace"
+nemus -- "Set up a workspace for the billing migration"
+```
+
+## How It Works
+
+1. Launches Claude Code CLI with a system prompt describing all available MCP tools
+2. Claude interprets the natural language request
+3. Claude uses MCP tools (create-workspace, search-repos, etc.) to fulfill the request
+4. Results are presented conversationally
+
+## Prerequisites
+
+- Claude Code CLI must be installed (`claude` command available)
+- MCP server should be installed (`nemus mcp install`)
+
+## When to Suggest
+
+- User wants to manage workspaces conversationally
+- User describes a complex workspace setup in natural language
+- User is new to the CLI and prefers natural language
+
+## Notes
+
+- The shell integration treats `nemus --` as a create-like command — if a workspace is created, it auto-CDs into it.
+- This is interactive-only and requires a TTY.

package/skills/workspace-manager/references/analyze-deps.md

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+# Analyze Dependencies
+
+Analyze inter-repository dependencies within a workspace and detect circular dependencies.
+
+## Instructions
+
+```bash
+nemus analyze-deps <workspace>
+```
+
+Alias:
+```bash
+w ad <workspace>
+```
+
+Without a workspace name, prompts interactively:
+```bash
+nemus analyze-deps
+```
+
+## What It Analyzes
+
+- `package.json` dependencies (npm packages that match workspace repo names)
+- `Dockerfile` references
+- `docker-compose.yml` service references
+
+## Output
+
+- **Dependency graph** — which repos depend on which
+- **Circular dependencies** — cycles detected with explanation
+- **Missing dependencies** — repos referenced but not in the workspace
+- **Mermaid diagram** — visual dependency graph
+- Optionally saves analysis to workspace metadata
+
+## Suggested Follow-ups
+
+- Missing dependencies: `nemus update --workspace <name> --repos <missing>` to add them
+- Circular dependencies: explain resolution strategies
+- For documentation: `nemus generate-docs <name>` to include the dependency graph
+
+## Success Criteria
+
+- Dependency analysis is presented with per-repo dependency lists.
+- Circular dependencies are highlighted if detected.
+- Missing repos are identified.

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

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+# Archive Workspace
+
+Archive a workspace to hide it from default listings. Archived workspaces auto-delete after 30 days.
+
+## Instructions
+
+### Archive
+```bash
+nemus archive --workspace <name> --yes
+```
+
+### Unarchive
+```bash
+nemus archive --unarchive --workspace <name> --yes
+```
+
+To list archived workspaces first:
+```bash
+nemus list --archived
+```
+
+## Flags
+
+| Flag | Short | Description |
+|---|---|---|
+| `--workspace <name>` | `-w` | Workspace name(s), comma-separated for multiple |
+| `--yes` | `-y` | Skip confirmation prompt |
+| `--unarchive` | | Restore instead of archive |
+
+## When to Suggest
+
+- Suggest archiving instead of deleting when the user may need the workspace later.
+- Suggest unarchiving when the user asks about a workspace that was recently archived.
+
+## Success Criteria
+
+- Workspace is hidden from default `nemus list` results.
+- User is aware of the 30-day auto-delete policy.

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

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+# Branch Create
+
+Create a new branch across all repositories in a workspace.
+
+## Instructions
+
+```bash
+nemus branch create --workspace <name> --branch <branch-name>
+nemus branch create --workspace <name> --branch <branch-name> --base <base-branch>
+```
+
+Or with positional args (legacy):
+```bash
+nemus branch create <workspace> <branch-name>
+nemus branch create <workspace> <branch-name> --base <base-branch> --force
+```
+
+## Flags
+
+| Flag | Short | Description |
+|---|---|---|
+| `--workspace <name>` | `-w` | Target workspace |
+| `--branch <name>` | `-b` | New branch name |
+| `--base <branch>` | | Base branch to create from (default: current branch) |
+| `--force` | | Force create even if branch exists |
+
+After creation, run `nemus status <name>` to verify all repos are on the new branch.
+
+## Success Criteria
+
+- New branch is created in all repos and per-repo results are reported.

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

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+# Branch Merge
+
+Merge a source branch into a target branch across all repositories in a workspace.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus branch merge <workspace> <source-branch> <target-branch> [--no-ff|--ff-only|--squash]
+   ```
+
+2. Present results per repo:
+   - Which repos merged successfully
+   - Which repos failed (e.g., conflicts)
+   - Summary count
+
+3. If there are merge conflicts, suggest the user resolve them manually in the affected repos.
+
+## Success Criteria
+
+- Merge is attempted in all repos.
+- Results are reported per repo with success/failure status.

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

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+# Branch Rebase
+
+Rebase all repositories in a workspace onto a target branch.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus branch rebase <workspace> <target-branch>
+   ```
+
+2. Present results per repo:
+   - Which repos rebased successfully
+   - Which repos failed (e.g., conflicts)
+   - Summary count
+
+3. If there are rebase conflicts, suggest the user resolve them manually in the affected repos.
+
+## Success Criteria
+
+- Rebase is attempted in all repos.
+- Results are reported per repo with success/failure status.

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

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+# Cache Clear
+
+Clear the local GitHub repository cache. A new cache will be created automatically on next fetch.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus cache clear
+   ```
+
+2. Confirm the cache was cleared.
+
+3. Suggest `nemus cache refresh` if the user wants to immediately rebuild the cache.
+
+## Success Criteria
+
+- Cache is cleared successfully.

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

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+# Cache Info
+
+View cache statistics including repo count, age, and size.
+
+## Instructions
+
+1. Run:
+   ```bash
+   nemus cache info
+   ```
+
+2. Report:
+   - Whether cache exists
+   - Number of cached repositories
+   - Last updated time
+   - Cache size
+
+3. If cache is stale or missing, suggest `nemus cache refresh`.
+
+## Success Criteria
+
+- Cache statistics are displayed.

package/skills/workspace-manager/references/configure-claude.md

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+# Configure Claude
+
+Configure Claude Code integration settings.
+
+## Instructions
+
+```bash
+nemus configure-claude
+```
+
+Alias:
+```bash
+w cc
+```
+
+## Settings
+
+| Setting | Description | Default |
+|---|---|---|
+| Auto-launch Claude | Launch Claude Code after workspace creation | `true` |
+| Generate context | Create `.claude.md` context file in workspaces | `true` |
+
+## Notes
+
+- This is interactive-only — there are no non-interactive flags.
+- The `.claude.md` file provides workspace context to Claude Code sessions.
+- Auto-launch requires the Claude Code CLI to be installed.
+
+## Success Criteria
+
+- Claude integration settings are updated.

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

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+# Configure
+
+Configure workspace-manager global settings interactively.
+
+## Instructions
+
+```bash
+nemus configure
+```
+
+Alias:
+```bash
+w cfg
+```
+
+## Settings
+
+| Setting | Description | Default |
+|---|---|---|
+| Workspaces directory | Where workspaces are stored | `~/workspaces` |
+| GitHub organization | Org to fetch repos from | `your-org` |
+| Clone protocol | SSH or HTTPS | `ssh` |
+| Auto-launch Claude | Launch Claude after workspace creation | `true` |
+| Generate .claude.md | Create context file in workspaces | `true` |
+| MCP server | Install MCP server for Claude integration | `true` |
+
+## Notes
+
+- Changing the GitHub org clears the repo cache automatically.
+- Enabling MCP after disabling it triggers an automatic install.
+- This is interactive-only — there are no non-interactive flags.
+
+## Success Criteria
+
+- User's settings are saved to `~/.workspace-manager-cache/config.json`.

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

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+# Create Workspace
+
+Create a new workspace with specified repositories.
+
+## Instructions
+
+1. If the user hasn't specified which repos they want, help them discover repos:
+   - Run `nemus cache search <query>` to search by name or description.
+   - Run `nemus cache list` to browse all available repos.
+   - Run `nemus suite list` to see pre-defined repo collections.
+
+2. Run the command with flags (non-interactive):
+   ```bash
+   nemus create --workspace <name> --repos <r1,r2,...> --yes
+   ```
+
+   Or interactively (no flags needed — CLI will prompt):
+   ```bash
+   nemus create
+   ```
+
+3. After creation, suggest next steps:
+   - `nemgo <name>` to navigate to the workspace (requires shell integration)
+   - Run `nemus status <name>` to check the initial state
+   - Run `nemus sync <name>` to pull latest changes
+
+## Flags
+
+| Flag | Short | Description |
+|---|---|---|
+| `--workspace <name>` | `-w` | Workspace name |
+| `--repos <r1,r2,...>` | `-r` | Comma-separated repo names |
+| `--yes` | `-y` | Skip confirmation prompt; also skips auto-launching the AI agent afterward, so the command is safe to run as a one-shot/non-interactive call |
+
+## Examples
+
+```bash
+nemus create --workspace payments --repos partnerships-api,payments-db --yes
+nemus suite use --suite platform --workspace platform-ws --yes
+```
+
+## Success Criteria
+
+- Workspace directory exists with all requested repos cloned.
+- User is informed of the workspace path and suggested next steps.

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

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+# Dashboard
+
+Launch a tmux-based multi-agent management dashboard for monitoring and controlling Claude agents across workspaces.
+
+## Instructions
+
+```bash
+nemus dashboard
+nemus dash
+```
+
+Opens a tmux session with a sidebar showing active agents and their status. Agent panes are on the right.
+
+## Options
+
+| Flag | Description |
+|---|---|
+| `--install-hooks` | Install Claude status hooks without launching dashboard |
+| `--uninstall-hooks` | Remove dashboard hooks from Claude settings |
+| `--list` | List running agents as JSON (non-interactive) |
+| `--status` | Show agent status summary (non-interactive) |
+| `--kill <sessionId>` | Kill agent by session ID (non-interactive) |
+| `--launch <workspace>` | Launch agent in workspace (non-interactive) |
+
+## Keyboard Shortcuts (sidebar)
+
+| Key | Action |
+|---|---|
+| `↑` / `↓` | Select agent |
+| `f` / `Enter` | Focus selected agent pane |
+| `z` | Toggle zoom on selected agent (hides others) |
+| `x` | Kill selected agent |
+| `n` | Launch new agent (workspace picker) |
+| `s` | Resume a previous Claude session |
+| `r` | Reset layout |
+| `q` | Detach — agents keep running in background |
+| `Q` | Quit all — kills session and all agents |
+
+## From any agent pane
+
+| Key | Action |
+|---|---|
+| `prefix+M` | Return to sidebar / reset layout |
+
+## Prerequisites
+
+- `tmux` must be installed (`brew install tmux`)
+- Claude CLI must be available for agent launching
+
+## Features
+
+- Real-time agent status via Claude Code hooks (idle/working/waiting/stopped)
+- Session persistence: `q` detaches, `nemus dash` reconnects
+- Zoom mode: selected agent takes full right side, others hidden
+- Session resume picker (`s`) with fuzzy search
+- Auto-installs Claude hooks on first run
+
+## Success Criteria
+
+- Tmux dashboard opens with sidebar and agent panes.
+- Agents can be launched, monitored, focused, zoomed, and killed from the dashboard.

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

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+# Delete Workspace
+
+Permanently delete one or more workspaces and all their cloned repositories.
+
+## Instructions
+
+1. **Confirm with the user before deleting.** This is a destructive, irreversible operation.
+
+2. Warn the user about any uncommitted changes — run `nemus status <name>` to check first.
+
+3. Run the command:
+   ```bash
+   nemus delete --workspace <name> --yes
+   ```
+
+   For multiple workspaces (comma-separated):
+   ```bash
+   nemus delete --workspace <name1>,<name2> --yes
+   ```
+
+4. Consider suggesting `nemus archive --workspace <name> --yes` as an alternative.
+
+## Flags
+
+| Flag | Short | Description |
+|---|---|---|
+| `--workspace <name>` | `-w` | Workspace name(s), comma-separated for multiple |
+| `--yes` | `-y` | Skip confirmation prompt |
+
+## Success Criteria
+
+- Workspace directory and all cloned repos are removed from disk.
+- User received explicit confirmation before deletion (unless `--yes` was passed).