fix(init): --hook installs hooks, and an absent MCP server is not a fault

[fajarhide]

omni init --hook has read "Only install hooks" since it shipped and registered the MCP
server as well. The parser accepted the flag and the code ignored it, which is #151 wearing
a different name. Then omni doctor called the state that flag produces a broken install
and pushed MCP Server is not configured. Run omni init, and omni doctor --fix
reinstalled it. Three ways of overruling a choice the CLI offered in the first place.

--hook and --mcp now install the half they name. Naming the host, naming both halves,
or naming neither still installs both, which is the table:

flags	hooks	mcp
--hook	yes	no
--mcp	no	yes
--hook --mcp	yes	yes
--claude, --all, or neither	yes	yes

An absent MCP registration on Claude Code is now reported as what it is rather than as a
fault, and --fix does not repair what nobody broke. That is not leniency: on this host the
hooks are what shortens output, while the MCP server is a convenience whose two tool
definitions sit in the prefix of every request, and the host discards the whole prompt
cache when an MCP server connects or disconnects with its tools loaded (#740). Wanting one
without the other is an ordinary preference.

docs/website in both trees stops telling readers to delete a line from ~/.claude.json
and warning them it will not stick, since there is a flag now.

The first test I wrote was toothless and is not in this PR. It asserted that the hooks
half leaves mcpServers out of settings.json, which was already true on main because
the MCP registration lives in a different file. The decision is a function now,
claude_halves, and the test is the table above. Break-tested: forcing it to answer
(true, true) fails at claude_halves(false, false, true, false) has to be (true, false).

Verification: make ci green, smoke_test.sh 70/70, check_translations.sh green.

Closes #757

Greptile Summary

This PR separates Claude hook and MCP installation so --hook and --mcp can install only their named half, and makes an absent Claude MCP registration informational rather than unhealthy.

• Adds table-driven selection for full, hooks-only, and MCP-only Claude setup.
• Extracts the Claude hook installer from the full integration installer.
• Stops doctor from warning about or directly repairing an absent optional MCP server.
• Updates English and Indonesian agent documentation and the changelog.

Confidence Score: 4/5

The PR should not merge until Claude hook repair preserves a hooks-only installation instead of restoring the optional MCP server.

The primary init path correctly separates the two installation halves, but every Claude hook-repair path still calls the full installer and therefore reverses the new hooks-only choice.

Files Needing Attention: src/agents/claude.rs

Important Files Changed

Filename	Overview
src/cli/init.rs	Adds Claude half-selection and routes single-half requests to dedicated installers.
src/agents/claude.rs	Splits hook installation and makes MCP absence optional, but hook repair still invokes the full installer and restores MCP.
docs/website/src/reference/agents.md	Documents hooks-only and MCP-only Claude setup in English.
docs/website/src-id/reference/agents.md	Mirrors the updated Claude setup guidance in Indonesian.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
  A[omni init flags] --> B{Claude halves}
  B -->|hook only| C[Install Claude hooks]
  B -->|MCP only| D[Register MCP server]
  B -->|both| E[Full Claude installer]
  F[omni doctor --fix] --> G{Hooks need repair?}
  G -->|yes| E
  E --> C
  E --> D

Loading

Comments Outside Diff (1)

1. src/agents/claude.rs, line 177 (link)

   Hook repair restores MCP

   When a hooks-only installation has missing hooks and the user runs omni doctor --fix, this branch calls the full install() method, which also registers the MCP server, causing .claude.json to regain the entry that --hook was intended to omit. The other hook-repair branches have the same behavior.

   Knowledge Base Used:

   • CLI command workflows
   • Agent integration layer
   Prompt To Fix With AI

   This is a comment left during a code review.
   Path: src/agents/claude.rs
   Line: 177
   
   Comment:
   **Hook repair restores MCP**
   
   When a hooks-only installation has missing hooks and the user runs `omni doctor --fix`, this branch calls the full `install()` method, which also registers the MCP server, causing `.claude.json` to regain the entry that `--hook` was intended to omit. The other hook-repair branches have the same behavior.
   
   **Knowledge Base Used:**
   - [CLI command workflows](https://app.greptile.com/weekndlabs/-/custom-context/knowledge-base/fajarhide/omni/-/docs/cli-command-workflows.md)
   - [Agent integration layer](https://app.greptile.com/weekndlabs/-/custom-context/knowledge-base/fajarhide/omni/-/docs/agent-integration-layer.md)
   
   ---
   
   For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

   

Prompt To Fix All With AI

### Issue 1
src/agents/claude.rs:177
**Hook repair restores MCP**

When a hooks-only installation has missing hooks and the user runs `omni doctor --fix`, this branch calls the full `install()` method, which also registers the MCP server, causing `.claude.json` to regain the entry that `--hook` was intended to omit. The other hook-repair branches have the same behavior.

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "docs(manual): the hooks-only route is a ..." | Re-trigger Greptile}

Context used (3)

• Knowledge Base — CLI command workflows
• Knowledge Base — Agent integration layer
• Knowledge Base — Agent adapters and output handling