Merge remote-tracking branch 'origin/main' into feat/pi-extension

# Conflicts:
#	README.md
#	src/cli/src/commands/config.ts
#	src/cli/src/commands/skills.ts

README.md

@@ -113,7 +113,64 @@ This writes a `.mcp.json` that tells Claude Code to connect through mcplocal. Re
 mcpctl console monitoring   # Preview what Claude sees
 ```
 
-### 7. Use mcpctl with pi (no MCP client, no Claude)
+### Connect prime-agent
+
+Prime-agent (Claude's open-source counterpart) talks to the same proxy MCP
+gateway over HTTP rather than stdio. Register a project and sync its skills
+into `~/.prime/agent/`:
+
+```bash
+mcpctl config prime-agent --project monitoring
+```
+
+This:
+
+1. Provisions the project's bearer credential in `~/.prime/agent/auth.json`
+   (`mcp:monitoring`, written 0600) — either from `--token <pat>`, an existing
+   entry that is still active server-side, or a freshly minted project token.
+   This happens first: if no credential can be provisioned the command stops
+   here with a non-zero exit and leaves `settings.json` alone, so the project
+   you are currently on keeps working.
+2. Registers the proxy MCP gateway in `~/.prime/agent/settings.json` as
+   `mcpServers.monitoring = { "type": "http", "url": "https://mcp.ad.itaz.eu/projects/monitoring/mcp" }`
+   (merging with any existing servers and preserving all other settings), and
+   unmounts the previously active mcpctl project so exactly one is live.
+   Servers you configured by hand are never touched.
+3. Writes a `.mcpctl-project` marker (only if none exists higher up, and never
+   from `$HOME`) so later syncs resolve the project. Skip with `--skip-marker`.
+4. Syncs the project's skills into `~/.prime/agent/skills/<name>/` as markdown
+   skills. The shared tree is ownership-tracked per project: it never deletes
+   another project's skills or an untracked hand-authored skill.
+5. Installs a `/mcpctl` project-switcher extension into
+   `~/.prime/agent/extensions/` so you can switch mcpctl projects from inside
+   the prime-agent UI (skip with `--skip-extension`).
+
+Re-sync later with:
+
+```bash
+mcpctl skills sync --agent prime-agent --project monitoring
+```
+
+Skip individual steps as needed:
+
+```bash
+mcpctl config prime-agent --project monitoring --token mcpctl_pat_xxx   # provide token, don't mint
+mcpctl config prime-agent --project monitoring --skip-skills            # don't sync skills
+mcpctl config prime-agent --project monitoring --skip-extension         # don't install /mcpctl switcher
+mcpctl config prime-agent --project monitoring --skip-marker            # don't touch .mcpctl-project here
+```
+
+The `/mcpctl` switcher runs with `--skip-extension --skip-marker`, so switching
+projects from inside prime-agent never re-scopes whichever repository
+prime-agent happened to be started in.
+
+Preview the change without writing anything:
+
+```bash
+mcpctl config prime-agent --project monitoring --dry-run
+```
+
+### Connect pi
 
 [pi](https://github.com/earendil-works/pi) does not support MCP, but it supports
 **extensions** and **skills**. mcpctl ships a native pi integration that talks
@@ -134,6 +191,7 @@ Inside pi:
 
 - `/mcpctl` — status, **switch project** (from the GUI), refresh tools, sync skills
 - gated projects auto-ungate: call `begin_session` once and the full tool set opens
+- re-sync with `mcpctl skills sync --agent pi --project monitoring`
 
 See [docs/pi-extension.md](docs/pi-extension.md) for full details.