fix(§22/registry): prune projects absent from the registry on reconcile (v0.55.0)

The registry mirror was additive-only — it upserted the projects/collections a
deployment's projects.yaml declares but never removed ones it had dropped.
Re-pinning to a different registry stranded the old project's collections + its
cached entries as dead rows that, at scale, starved writes (PPE accumulated
~1.2k orphaned entry rows and had to be reset by hand).

`registry.refresh_registry(prune=True)` now calls `projects.prune_absent_projects`,
deleting a removed project with its collections and every project-scoped row
(the 7 project_id-keyed tables + 13 collection_id-keyed entry-corpus tables +
the non-keyed thread_messages descendant) in one FK-off transaction with a
`PRAGMA foreign_key_check` backstop that rolls back rather than leave a dangling
ref — mirroring restamp_default_project / reconcile_default_collection_id.

Scoped for safety: whole-project granularity (a present project is untouched);
the default project is never pruned; prune runs ONLY on the full-reconcile
triggers (startup + the periodic sweep), never on incidental refreshes (collection
create, webhook), so an in-app refresh can't wipe a project. Reached only after a
successful parse of a non-empty registry (parse_registry rejects empty; the read
raises on transport error), so a transient read can't trigger a wipe.

Second of the two §9-surfaced framework fragilities. No migration. backend 685
green (+5: prune removes-all/no-op/never-default/empty-rejected/incidental-no-prune
with FK-integrity backstop).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

backend/app/registry.py

@@ -333,11 +333,18 @@ async def _mirror_named_collections(config: Config, gitea: Gitea, doc: RegistryD
             _upsert_named_collection(proj, subdir, ce, sha)
 
 
-async def refresh_registry(config: Config, gitea: Gitea) -> None:
+async def refresh_registry(config: Config, gitea: Gitea, *, prune: bool = False) -> None:
     """Mirror REGISTRY_REPO/projects.yaml into projects + deployment.
 
     Idempotent. Raises RegistryError on a missing/invalid file and GiteaError
     on transport failure; the caller chooses fatal-vs-tolerated.
+
+    `prune=True` additionally removes projects the registry no longer declares
+    (and their collections + entries) — see `projects.prune_absent_projects`.
+    It is OFF by default and enabled only on the full-reconcile triggers
+    (startup + the periodic sweep), never on incidental refreshes (a collection
+    create, a webhook) that don't change the project set — keeping the
+    destructive sweep on the few code paths that mean "reconcile to the registry."
     """
     item = await gitea.get_contents(
         config.gitea_org, config.registry_repo, "projects.yaml", ref="main"
@@ -355,4 +362,18 @@ async def refresh_registry(config: Config, gitea: Gitea) -> None:
     apply_registry(doc, sha, projects_mod.resolved_default_id(config))
     # §22 S2: discover + upsert named collections from each content repo.
     await _mirror_named_collections(config, gitea, doc, sha)
-    log.info("registry: mirrored %d project(s) at %s", len(doc.projects), sha)
+    # Prune projects the registry no longer declares (additive-only was a §9
+    # fragility — a re-pin to a new registry stranded the old projects' entries,
+    # starving writes). Safe here: we only reach this line after a successful
+    # parse of a non-empty registry (parse_registry rejects an empty project list
+    # and the read above raises on transport failure), so a transient failure
+    # never prunes. Whole-project granularity; the default project is never pruned.
+    pruned = (
+        projects_mod.prune_absent_projects(config, {e.id for e in doc.projects})
+        if prune else []
+    )
+    log.info(
+        "registry: mirrored %d project(s) at %s%s",
+        len(doc.projects), sha,
+        f"; pruned {len(pruned)} absent: {pruned}" if pruned else "",
+    )