feat: BOM auto-extraction and manifest field population (#276, #277)

Documentation updates:
- KNOWN_ISSUES.md: correct #6 (datum handling), resolve #10
  (delete_bom_entry) and #11 (silo icons), fix stale formatDate
  reference, mark completed next steps, add new next steps.
- INTEGRATION_PLAN.md: correct ztools SDK migration claim.

kc_format.py (#277):
- New _manifest_enrich_hook: populates part_uuid from SiloItemId and
  silo_instance from Silo API URL on every .kc save.
- New update_manifest_fields(): public API to update manifest fields
  in an already-saved .kc ZIP (used for post-upload revision_hash).

mods/silo submodule (#276):
- New bom_sync.py extraction engine.
- Post-commit hooks for BOM sync and manifest revision update.
- SSE bom_merged signal + Activity pane handler.
- merge_bom_json client method (forward-looking).

Refs: #276, #277

docs/INTEGRATION_PLAN.md

@@ -111,7 +111,7 @@ Pure Python addons with `package.xml` manifests. Self-contained with `Init.py`,
 
 **Implementation:** `mods/sdk/kindred_sdk/` package with wrappers for editing contexts, theme tokens, FileOrigin registration, and dock panel creation. YAML-driven palette system (`palettes/catppuccin-mocha.yaml`) replaces hardcoded color dicts that were duplicated across 5+ locations.
 
-**Migration:** Both ztools and Silo have been migrated to use the SDK (#250). No addon code calls `FreeCADGui.registerEditingOverlay()`, `FreeCADGui.addOrigin()`, or defines hardcoded MOCHA dicts directly.
+**Migration:** Silo has been migrated to use the SDK (#250) — it declares `<dependency>sdk</dependency>` and uses `kindred_sdk` for overlay registration and theme tokens. ztools has **not yet been migrated**: its `package.xml` lacks `<kindred>` metadata and its `InitGui.py` does not import from `kindred_sdk`. See KNOWN_ISSUES.md next step #9.
 
 ### Phase 1.75: C++ module scaffold -- DONE
 

docs/KNOWN_ISSUES.md

@@ -16,7 +16,7 @@
 
 5. **No unit tests.** Zero test coverage for ztools and Silo FreeCAD commands. Silo Go backend also lacks tests.
 
-6. **Assembly solver datum handling is minimal.** The `findPlacement()` fix in `src/Mod/Assembly/UtilsAssembly.py` extracts placement from `obj.Shape.Faces[0]` for `PartDesign::Plane` and from shape vertex for `PartDesign::Point`. Does not handle empty shapes or non-planar datum objects.
+6. **Assembly solver datum handling is minimal.** `UtilsAssembly.findPlacement()` handles standard shapes (faces, edges, vertices) and `App::Line` origin objects. It does not extract placement from `PartDesign::Plane` or `PartDesign::Point` datum objects — when no element is selected, it returns a default `App.Placement()`. This means assembly joints referencing datum planes/points may produce incorrect placement.
 
 ### Medium
 
@@ -26,9 +26,9 @@
 
 9. **tangent_to_cylinder falls back to manual placement.** TangentPlane MapMode requires a vertex reference not collected by the current UI.
 
-10. **`delete_bom_entry()` bypasses error normalization.** Uses raw `urllib.request` instead of `SiloClient._request()`.
+10. ~~**`delete_bom_entry()` bypasses error normalization.**~~ Resolved. `delete_bom_entry()` uses `self._request("DELETE", ...)` which routes through `SiloClient._request()` with proper error handling.
 
-11. **Missing Silo icons.** Three commands reference icons that don't exist: `silo-tag.svg` (`Silo_TagProjects`), `silo-rollback.svg` (`Silo_Rollback`), `silo-status.svg` (`Silo_SetStatus`). The `_icon()` function returns an empty string, so these commands render without toolbar icons.
+11. ~~**Missing Silo icons.**~~ Resolved. All three icons now exist: `silo-tag.svg`, `silo-rollback.svg`, `silo-status.svg` in `mods/silo/freecad/resources/icons/`.
 
 ### Fixed (retain for reference)
 
@@ -50,7 +50,7 @@
 | CSRF protection | Implemented | `nosurf` library on web form routes |
 | File locking | Not implemented | Needed to prevent concurrent edits |
 | Odoo ERP integration | Stub only | Returns "not yet implemented" |
-| Part number date segments | Broken | `formatDate()` returns error |
+| Part number date segments | Unknown | `formatDate()` reference is stale — function not found in codebase |
 | Location/inventory APIs | Tables exist, no handlers | |
 | CSV import rollback | Not implemented | `bom_handlers.go` |
 | SSE event streaming | Implemented | Reconnect logic with exponential backoff |
@@ -71,14 +71,20 @@
 
 1. **Authentication hardening** -- Deploy FreeIPA and Keycloak infrastructure. End-to-end test LDAP and OIDC flows. Harden token rotation and session expiry.
 
-2. **BOM-Assembly bridge** -- Auto-populate Silo BOM from Assembly component links on save.
+2. **BOM-Assembly bridge** -- Auto-populate Silo BOM from Assembly component links on save. See `docs/BOM_MERGE.md` for specification.
 
 3. **File locking** -- Pessimistic locks on `Silo_Open` to prevent concurrent edits. Requires server-side lock table and client-side lock display.
 
-4. **Build system** -- CMake install rules for `mods/` submodules so packages include ztools and Silo without manual steps.
+4. ~~**Build system**~~ Done. CMake install rules in `src/Mod/Create/CMakeLists.txt` handle all `mods/` submodules.
 
 5. **Test coverage** -- Unit tests for ztools datum creation, Silo FreeCAD commands, and Go API endpoints.
 
-6. **QSS consolidation** -- Eliminate the 3-copy QSS duplication via build-time copy or symlinks. The canonical source is `resources/preferences/KindredCreate/KindredCreate.qss`.
+6. ~~**QSS consolidation**~~ Done. Canonical QSS is `src/Gui/Stylesheets/KindredCreate.qss`; PreferencePacks copy generated at build time via `configure_file()`.
 
-7. **Update notification UI** -- Display in-app notification when a new release is available (issue #30). The update checker backend is already implemented.
+7. **Update notification UI** -- Display in-app notification when a new release is available (issue #30). The update checker backend (`update_checker.py`) runs at startup; notification UI still needed.
+
+8. **KC file format completion** -- Populate `silo_instance` and `revision_hash` in manifest.json. Implement write-back for history.json, approvals.json, dependencies.json. See `docs/KC_SPECIFICATION.md`.
+
+9. **ztools SDK migration** -- Add `<kindred>` metadata to `mods/ztools/package.xml` (load priority, version bounds, SDK dependency). Migrate `InitGui.py` to use `kindred_sdk` APIs for context/overlay registration.
+
+10. **DAG cross-item edges** -- Assembly constraints referencing geometry in child parts should populate `dag_cross_edges`. Deferred until assembly constraint model is finalized.

src/Mod/Create/kc_format.py

@@ -45,6 +45,51 @@ def _metadata_save_hook(doc, filename, entries):
 register_pre_reinject(_metadata_save_hook)
 
 
+def _manifest_enrich_hook(doc, filename, entries):
+    """Populate silo_instance and part_uuid from the tracked Silo object."""
+    raw = entries.get("silo/manifest.json")
+    if raw is None:
+        return
+    try:
+        manifest = json.loads(raw)
+    except (json.JSONDecodeError, ValueError):
+        return
+
+    changed = False
+
+    # Populate part_uuid from SiloItemId if available.
+    for obj in doc.Objects:
+        if hasattr(obj, "SiloItemId") and obj.SiloItemId:
+            if manifest.get("part_uuid") != obj.SiloItemId:
+                manifest["part_uuid"] = obj.SiloItemId
+                changed = True
+            break
+
+    # Populate silo_instance from Silo settings.
+    if not manifest.get("silo_instance"):
+        try:
+            import silo_commands
+
+            api_url = silo_commands._get_api_url()
+            if api_url:
+                # Strip /api suffix to get base instance URL.
+                instance = api_url.rstrip("/")
+                if instance.endswith("/api"):
+                    instance = instance[:-4]
+                manifest["silo_instance"] = instance
+                changed = True
+        except Exception:
+            pass
+
+    if changed:
+        entries["silo/manifest.json"] = (json.dumps(manifest, indent=2) + "\n").encode(
+            "utf-8"
+        )
+
+
+register_pre_reinject(_manifest_enrich_hook)
+
+
 KC_VERSION = "1.0"
 
 
@@ -133,6 +178,34 @@ class _KcFormatObserver:
             )
 
 
+def update_manifest_fields(filename, updates):
+    """Update fields in an existing .kc manifest after save.
+
+    *filename*: path to the .kc file.
+    *updates*: dict of field_name -> value to merge into the manifest.
+
+    Used by silo_commands to write ``revision_hash`` after a successful
+    upload (which happens after the ZIP has already been written by save).
+    """
+    if not filename or not filename.lower().endswith(".kc"):
+        return
+    if not os.path.isfile(filename):
+        return
+    try:
+        with zipfile.ZipFile(filename, "a") as zf:
+            if "silo/manifest.json" not in zf.namelist():
+                return
+            raw = zf.read("silo/manifest.json")
+            manifest = json.loads(raw)
+            manifest.update(updates)
+            zf.writestr(
+                "silo/manifest.json",
+                json.dumps(manifest, indent=2) + "\n",
+            )
+    except Exception as e:
+        FreeCAD.Console.PrintWarning(f"kc_format: failed to update manifest: {e}\n")
+
+
 def register():
     """Connect to application-level save signals."""
     FreeCAD.addDocumentObserver(_KcFormatObserver())