docs(bootstrap): clarify three-step Docker first-boot flow

Rework README and docker-compose comments to document the deliberate
chicken-and-egg escape: the `init` sidecar now only runs `migrate` and
`load_library_types`, leaving `setup_neo4j_indexes` as a manual step
after the system embedding model is configured in `/admin/`. This
avoids making `app` unreachable on first boot when no embedding model
row exists yet, while preserving loud failure on dimension mismatch.

mnemosyne/library/apps.py

@@ -11,8 +11,13 @@ the stderr of a different container.
 
 The probe is deliberately best-effort: it cannot crash the process even if
 Neo4j is unreachable, because a transient DB blip on startup should not
-take down the whole app. The `init` sidecar is the hard gate; this is the
-second line of defence for long-running containers.
+take down the whole app. Nothing hard-gates on the vector indexes — the
+``init`` sidecar only runs ``migrate`` + ``load_library_types`` (vector
+indexes cannot be created before the system embedding model is configured
+in the admin, which is a manual step after first boot). This probe is the
+only way an operator learns that the manual
+``setup_neo4j_indexes`` step was skipped or fell out of sync with the
+current system model.
 """
 
 import logging
@@ -149,9 +154,10 @@ def _run_startup_probe():
     for name in _EXPECTED_VECTOR_INDEXES:
         if name not in present:
             logger.error(
-                "Neo4j vector index '%s' is missing. Run "
-                "'docker compose run --rm init' (or 'python manage.py "
-                "setup_neo4j_indexes') to rebuild.",
+                "Neo4j vector index '%s' is missing. Configure the system "
+                "embedding model in /admin/llm_manager/llmmodel/, then run "
+                "'docker compose exec app python manage.py "
+                "setup_neo4j_indexes' to create it.",
                 name,
             )
             continue