wip(929): stage 5 — drop FS-based dep checks and qa-mode parser from io/story_metadata

Migrate the last three callers of the FS-scanning dependency helpers to the
CRDT-direct equivalents and delete the dead helpers:

- agents/pool/auto_assign/story_checks.rs: has_unmet_dependencies and
  check_archived_dependencies now wrap check_unmet_deps_crdt /
  check_archived_deps_crdt directly. Tests rewritten to seed the CRDT.
- http/mcp/story_tools/story/update.rs: bug-503 archived-dep warning now
  reads from CRDT instead of scanning 6_archived.
- agents/pool/pipeline/advance/helpers.rs: resolve_qa_mode_from_store is
  CRDT-only (the FS fallback for content-store-empty stories is gone).
- io/story_metadata/parser.rs: resolve_qa_mode_from_content removed.
- io/story_metadata/deps.rs: check_unmet_deps and dep_is_done deleted,
  along with the unused check_unmet_deps_from_list helper.
- io/story_metadata/mod.rs: re-exports trimmed accordingly.

check_archived_deps_from_list survives because story-creation still calls
it before the CRDT entry exists (used from story_tools/story/create.rs).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

server/src/http/mcp/story_tools/bug.rs

@@ -13,9 +13,7 @@ use crate::http::workflow::{
     list_refactor_files, load_pipeline_state, load_upcoming_stories, remove_criterion_from_file,
     update_story_in_file, validate_story_dirs,
 };
-use crate::io::story_metadata::{
-    check_archived_deps, check_archived_deps_from_list, parse_unchecked_todos,
-};
+use crate::io::story_metadata::{check_archived_deps_from_list, parse_unchecked_todos};
 use crate::service::story::parse_test_cases;
 use crate::slog_warn;
 #[allow(unused_imports)]

server/src/http/mcp/story_tools/criteria.rs

@@ -13,9 +13,7 @@ use crate::http::workflow::{
     list_refactor_files, load_pipeline_state, load_upcoming_stories, remove_criterion_from_file,
     update_story_in_file, validate_story_dirs,
 };
-use crate::io::story_metadata::{
-    check_archived_deps, check_archived_deps_from_list, parse_unchecked_todos,
-};
+use crate::io::story_metadata::{check_archived_deps_from_list, parse_unchecked_todos};
 use crate::service::story::parse_test_cases;
 use crate::slog_warn;
 #[allow(unused_imports)]

server/src/http/mcp/story_tools/refactor.rs

@@ -13,9 +13,7 @@ use crate::http::workflow::{
     list_refactor_files, load_pipeline_state, load_upcoming_stories, remove_criterion_from_file,
     update_story_in_file, validate_story_dirs,
 };
-use crate::io::story_metadata::{
-    check_archived_deps, check_archived_deps_from_list, parse_unchecked_todos,
-};
+use crate::io::story_metadata::{check_archived_deps_from_list, parse_unchecked_todos};
 use crate::service::story::parse_test_cases;
 use crate::slog_warn;
 #[allow(unused_imports)]

server/src/http/mcp/story_tools/spike.rs

@@ -13,9 +13,7 @@ use crate::http::workflow::{
     list_refactor_files, load_pipeline_state, load_upcoming_stories, remove_criterion_from_file,
     update_story_in_file, validate_story_dirs,
 };
-use crate::io::story_metadata::{
-    check_archived_deps, check_archived_deps_from_list, parse_unchecked_todos,
-};
+use crate::io::story_metadata::{check_archived_deps_from_list, parse_unchecked_todos};
 use crate::service::story::parse_test_cases;
 use crate::slog_warn;
 #[allow(unused_imports)]

server/src/http/mcp/story_tools/story/update.rs

@@ -2,7 +2,6 @@
 
 use crate::http::context::AppContext;
 use crate::http::workflow::update_story_in_file;
-use crate::io::story_metadata::check_archived_deps;
 use crate::slog_warn;
 use serde_json::Value;
 use std::collections::HashMap;
@@ -89,12 +88,8 @@ pub(crate) fn tool_update_story(args: &Value, ctx: &AppContext) -> Result<String
     }
 
     // Bug 503: warn if any depends_on in the (now updated) story points at an archived story.
-    let stage = crate::pipeline_state::read_typed(story_id)
-        .ok()
-        .flatten()
-        .map(|i| i.stage.dir_name().to_string())
-        .unwrap_or_else(|| "1_backlog".to_string());
-    let archived_deps = check_archived_deps(&root, &stage, story_id);
+    // Story 929: reads from the CRDT (was a FS-yaml scan).
+    let archived_deps = crate::crdt_state::check_archived_deps_crdt(story_id);
     if !archived_deps.is_empty() {
         slog_warn!(
             "[update-story] Story '{story_id}' depends_on {archived_deps:?} which \