Fixes#1578.
## What was wrong
Bootstrapping CodeGraph in a fresh environment — the issue's case is a throwaway container per AI session — took two commands, `codegraph install --yes` and then `codegraph init`, and the second one could still stop on a prompt (the gitignored-child-repos offer, the watch-fallback offer on WSL/`/mnt`). There was no way to wire agents and build the project's index in one non-interactive line.
The installer's "never index implicitly" rule is deliberate (a surprise index of `$HOME` is exactly what `init` refuses), so the gap is an explicit opt-in, not a change in default behavior.
## What this does
- **`codegraph install -i, --init`** — after wiring the agents, runs the `init` flow in the current directory. It also runs when nothing was wired (`--target none`, no agents detected), since the installer returns normally in that case. Every `init` guard applies: a home directory / filesystem root / parent of home is **refused with exit code 1** (no implied `--force`), and an already-initialized project just reports that and exits 0. `--print-config` and `--refresh` return before the install, so `--init` is a no-op with them.
- **`codegraph init -y, --yes`** — non-interactive: the ignored-repos offer prints its one-line `includeIgnored` opt-in snippet instead of prompting (the existing non-TTY behavior), and the watch-fallback offer takes its `yes` default. `install --init` passes `--yes` through, so `codegraph install --yes --init` is a fully unattended bootstrap.
- The `init` action body becomes `runInit()`, shared by both commands. The plain `init` path is behavior-identical (same refusal, already-initialized notice, supervised index, telemetry, offers, outro).
- The post-install "Next: index a project" note gains one line mentioning `--init`; README gets the flag row and a `--yes --init` example.
On the reporter's other observation — `install --yes` skipping the "install the CLI on your PATH" step: that's by design for scripted use (it assumes the CLI is already present), and the `bunx @colbymchenry/codegraph serve --mcp` MCP entry they found is the self-contained alternative. Not changed here.
## Tests
`__tests__/cli-install-init.test.ts` — end-to-end against the built binary with stdin closed (a blocking prompt would fail), always `--target none` so the suite never touches an agent config on the host:
- `install --yes --target none --init` → exit 0, installer reports nothing to wire, `Initialized in <tmp>`, `.codegraph/codegraph.db` exists;
- the same on an already-initialized project → `Already initialized`, exit 0;
- the same at the filesystem root → exit 1, `Refusing to initialize`, nothing written;
- `init --yes` with stdin closed → exit 0, index built;
- `init --help` lists `-y, --yes`, `install --help` lists `-i, --init`.
`npx vitest run __tests__/installer-targets.test.ts __tests__/upgrade.test.ts` → 283 passed, 3 skipped. Full `npm test` → see the checks on this PR / below.
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https://claude.ai/code/session_01LxZj6W6Y1SHXwvpT3uwJpK
