feat: unify bootstrap export and apply cli

bootstrap/README.md

@@ -13,20 +13,90 @@ The Linux Server design docs are the source specification:
 - `bundle-manifest.json` lists the canonical files and directories in the generic bundle.
 - `export-rules.json` defines which metadata is exported and which paths must verify.
 - `templates/generic/` holds the canonical bootstrap templates.
-- `generate-export.py` creates `bootstrap/exports/generic` from the manifest and rules.
+- `cli.py` is the unified bootstrap CLI.
+- `generate-export.py`, `init-project.py`, and `smoke-test.py` are compatibility wrappers.
+
+## CLI
+
+The long-term interface is the unified bootstrap CLI:
+
+```bash
+python3 bootstrap/cli.py export
+python3 bootstrap/cli.py verify
+python3 bootstrap/cli.py apply /path/to/project
+python3 bootstrap/cli.py smoke-test
+```
 
 ## Generate
 
 From a checked-out Agent OS clone:
 
 ```bash
-python3 bootstrap/generate-export.py
+python3 bootstrap/cli.py export
 ```
 
 To generate the live runtime export requested by the server workflow:
 
 ```bash
-sudo -n python3 bootstrap/generate-export.py --output /opt/agent-os/bootstrap/exports/generic
+sudo -n python3 bootstrap/cli.py export --output /opt/agent-os/bootstrap/exports/generic
 ```
 
 Generated exports are intentionally ignored by Git.
+
+To verify an existing bundle:
+
+```bash
+python3 bootstrap/cli.py verify --output /path/to/bootstrap/exports/generic
+```
+
+## Init / Apply
+
+Initialize or update a project root from the bootstrap bundle:
+
+```bash
+python3 bootstrap/cli.py apply /path/to/project
+```
+
+The default behavior is:
+
+- non-destructive
+- merge-aware
+- prompt-driven on conflicts
+
+Apply shows a summary first, then handles conflicts one file at a time.
+
+If a target file already exists and differs from the bootstrap content, the CLI offers:
+
+- `keep`
+- `replace`
+- `write-new`
+
+It also supports:
+
+- optional `diff` when the file is cheap to diff
+- `apply to all remaining conflicts` after choosing an action
+
+Bootstrap-managed files are tracked in `.agent-os-bootstrap-state.json` in the
+target project root.
+
+For unattended runs, you must choose an explicit policy:
+
+```bash
+python3 bootstrap/cli.py apply /path/to/project --on-conflict keep
+python3 bootstrap/cli.py apply /path/to/project --on-conflict replace
+python3 bootstrap/cli.py apply /path/to/project --on-conflict write-new
+```
+
+## Smoke Test
+
+Run the bootstrap against a brand new temp directory:
+
+```bash
+python3 bootstrap/cli.py smoke-test
+```
+
+To keep the generated temp folder for inspection:
+
+```bash
+python3 bootstrap/cli.py smoke-test --keep
+```