diff --git a/server/src/agents/pool/auto_assign/auto_assign.rs b/server/src/agents/pool/auto_assign/auto_assign.rs
index ad0c8f8f..261b9948 100644
--- a/server/src/agents/pool/auto_assign/auto_assign.rs
+++ b/server/src/agents/pool/auto_assign/auto_assign.rs
@@ -139,27 +139,15 @@ impl AgentPool {
                     );
                     let empty_diff_reason = "Feature branch has no code changes — the coder agent \
                          did not produce any commits.";
-                    // Write merge_failure and blocked to content store.
-                    if let Some(contents) = crate::db::read_content(story_id) {
-                        let updated = crate::io::story_metadata::write_merge_failure_in_content(
-                            &contents,
-                            empty_diff_reason,
-                        );
-                        let blocked = crate::io::story_metadata::write_blocked_in_content(&updated);
-                        crate::db::write_content(story_id, &blocked);
-                        crate::db::write_item_with_content(story_id, stage_dir, &blocked);
-                    } else {
-                        // Fallback: filesystem.
-                        let story_path = project_root
-                            .join(".huskies/work")
-                            .join(stage_dir)
-                            .join(format!("{story_id}.md"));
-                        let _ = crate::io::story_metadata::write_merge_failure(
-                            &story_path,
-                            empty_diff_reason,
-                        );
-                        let _ = crate::io::story_metadata::write_blocked(&story_path);
-                    }
+                    // Write merge_failure and blocked to content store + CRDT.
+                    let contents = crate::db::read_content(story_id)
+                        .unwrap_or_else(|| "---\nname: unknown\n---\n".to_string());
+                    let updated = crate::io::story_metadata::write_merge_failure_in_content(
+                        &contents,
+                        empty_diff_reason,
+                    );
+                    let blocked = crate::io::story_metadata::write_blocked_in_content(&updated);
+                    crate::db::write_item_with_content(story_id, stage_dir, &blocked);
                     let _ = self.watcher_tx.send(crate::io::watcher::WatcherEvent::StoryBlocked {
                         story_id: story_id.to_string(),
                         reason: empty_diff_reason.to_string(),
diff --git a/server/src/agents/pool/auto_assign/reconcile.rs b/server/src/agents/pool/auto_assign/reconcile.rs
index ec7f4284..53e30052 100644
--- a/server/src/agents/pool/auto_assign/reconcile.rs
+++ b/server/src/agents/pool/auto_assign/reconcile.rs
@@ -209,15 +209,10 @@ impl AgentPool {
                                 message: format!("Failed to advance to QA: {e}"),
                             });
                         } else {
-                            let story_path = project_root
-                                .join(".huskies/work/3_qa")
-                                .join(format!("{story_id}.md"));
-                            if let Err(e) =
-                                crate::io::story_metadata::write_review_hold(&story_path)
-                            {
-                                eprintln!(
-                                    "[startup:reconcile] Failed to set review_hold on '{story_id}': {e}"
-                                );
+                            // Set review_hold in the content store + CRDT.
+                            if let Some(contents) = crate::db::read_content(story_id) {
+                                let updated = crate::io::story_metadata::write_review_hold_in_content(&contents);
+                                crate::db::write_item_with_content(story_id, "3_qa", &updated);
                             }
                             eprintln!("[startup:reconcile] Moved '{story_id}' → 3_qa/ (qa: human — holding for review).");
                             let _ = progress_tx.send(ReconciliationEvent {
@@ -267,29 +262,25 @@ impl AgentPool {
                         if item_type == "spike" {
                             true
                         } else {
-                            let story_path = project_root
-                                .join(".huskies/work/3_qa")
-                                .join(format!("{story_id}.md"));
                             let default_qa = crate::config::ProjectConfig::load(project_root)
                                 .unwrap_or_default()
                                 .default_qa_mode();
-                            matches!(
-                                crate::io::story_metadata::resolve_qa_mode(&story_path, default_qa),
-                                crate::io::story_metadata::QaMode::Human
-                            )
+                            if let Some(contents) = crate::db::read_content(story_id) {
+                                matches!(
+                                    crate::io::story_metadata::resolve_qa_mode_from_content(&contents, default_qa),
+                                    crate::io::story_metadata::QaMode::Human
+                                )
+                            } else {
+                                matches!(default_qa, crate::io::story_metadata::QaMode::Human)
+                            }
                         }
                     };
 
                     if needs_human_review {
-                        let story_path = project_root
-                            .join(".huskies/work/3_qa")
-                            .join(format!("{story_id}.md"));
-                        if let Err(e) =
-                            crate::io::story_metadata::write_review_hold(&story_path)
-                        {
-                            eprintln!(
-                                "[startup:reconcile] Failed to set review_hold on '{story_id}': {e}"
-                            );
+                        // Set review_hold in the content store + CRDT.
+                        if let Some(contents) = crate::db::read_content(story_id) {
+                            let updated = crate::io::story_metadata::write_review_hold_in_content(&contents);
+                            crate::db::write_item_with_content(story_id, "3_qa", &updated);
                         }
                         eprintln!(
                             "[startup:reconcile] '{story_id}' passed QA — holding for human review."
diff --git a/server/src/chat/commands/depends.rs b/server/src/chat/commands/depends.rs
index 6af13d7f..56bcf485 100644
--- a/server/src/chat/commands/depends.rs
+++ b/server/src/chat/commands/depends.rs
@@ -7,7 +7,7 @@
 //! Passing no dependency numbers clears the field entirely.
 
 use super::CommandContext;
-use crate::io::story_metadata::{parse_front_matter, write_depends_on};
+use crate::io::story_metadata::{clear_front_matter_field_in_content, parse_front_matter, set_front_matter_field};
 
 /// Handle the `depends` command.
 ///
@@ -51,7 +51,7 @@ pub(super) fn handle_depends(ctx: &CommandContext) -> Option<String> {
     }
 
     // Find the story by numeric prefix: CRDT → content store → filesystem.
-    let (story_id, _stage_dir, path, content) =
+    let (story_id, stage_dir, _path, content) =
         match crate::chat::lookup::find_story_by_number(ctx.project_root, num_str) {
             Some(found) => found,
             None => {
@@ -61,24 +61,36 @@ pub(super) fn handle_depends(ctx: &CommandContext) -> Option<String> {
             }
         };
 
-    let story_name = content
-        .or_else(|| std::fs::read_to_string(&path).ok())
-        .and_then(|c| parse_front_matter(&c).ok())
+    let contents = match content.or_else(|| crate::db::read_content(&story_id)) {
+        Some(c) => c,
+        None => return Some(format!("No content found for **{story_id}**.")),
+    };
+
+    let story_name = parse_front_matter(&contents)
+        .ok()
         .and_then(|m| m.name)
         .unwrap_or_else(|| story_id.clone());
 
-    match write_depends_on(&path, &deps) {
-        Ok(()) if deps.is_empty() => Some(format!(
+    // Update depends_on in the content store + CRDT.
+    let updated = if deps.is_empty() {
+        clear_front_matter_field_in_content(&contents, "depends_on")
+    } else {
+        let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
+        let yaml_value = format!("[{}]", nums.join(", "));
+        set_front_matter_field(&contents, "depends_on", &yaml_value)
+    };
+    crate::db::write_item_with_content(&story_id, &stage_dir, &updated);
+
+    if deps.is_empty() {
+        Some(format!(
             "Cleared all dependencies for **{story_name}** ({story_id})."
-        )),
-        Ok(()) => {
-            let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
-            Some(format!(
-                "Set depends_on: [{}] for **{story_name}** ({story_id}).",
-                nums.join(", ")
-            ))
-        }
-        Err(e) => Some(format!("Failed to update dependencies for {story_id}: {e}")),
+        ))
+    } else {
+        let nums: Vec<String> = deps.iter().map(|n| n.to_string()).collect();
+        Some(format!(
+            "Set depends_on: [{}] for **{story_name}** ({story_id}).",
+            nums.join(", ")
+        ))
     }
 }
 
@@ -188,13 +200,11 @@ mod tests {
             output.contains("477") && output.contains("478"),
             "response should mention dep numbers: {output}"
         );
-        let contents = std::fs::read_to_string(
-            tmp.path().join(".huskies/work/1_backlog/42_story_foo.md"),
-        )
-        .unwrap();
+        let contents = crate::db::read_content("42_story_foo")
+            .expect("content store should have the story");
         assert!(
             contents.contains("depends_on: [477, 478]"),
-            "file should have depends_on set: {contents}"
+            "content store should have depends_on set: {contents}"
         );
     }
 
@@ -212,13 +222,11 @@ mod tests {
             output.contains("Cleared"),
             "should confirm clearing deps: {output}"
         );
-        let contents = std::fs::read_to_string(
-            tmp.path().join(".huskies/work/2_current/10_story_bar.md"),
-        )
-        .unwrap();
+        let contents = crate::db::read_content("10_story_bar")
+            .expect("content store should have the story");
         assert!(
             !contents.contains("depends_on"),
-            "file should have depends_on cleared: {contents}"
+            "content store should have depends_on cleared: {contents}"
         );
     }
 
diff --git a/server/src/chat/commands/unblock.rs b/server/src/chat/commands/unblock.rs
index 8082652a..6f967ac0 100644
--- a/server/src/chat/commands/unblock.rs
+++ b/server/src/chat/commands/unblock.rs
@@ -5,7 +5,7 @@
 //! and returns a confirmation.
 
 use super::CommandContext;
-use crate::io::story_metadata::{clear_front_matter_field, clear_front_matter_field_in_content, parse_front_matter, set_front_matter_field};
+use crate::io::story_metadata::{clear_front_matter_field_in_content, parse_front_matter, set_front_matter_field};
 use std::path::Path;
 
 /// Handle the `unblock` command.
@@ -33,7 +33,7 @@ pub(super) fn handle_unblock(ctx: &CommandContext) -> Option<String> {
 ///
 /// Lookup priority: CRDT → content store → filesystem (Story 512).
 pub(crate) fn unblock_by_number(project_root: &Path, story_number: &str) -> String {
-    let (story_id, _stage_dir, path, _content) =
+    let (story_id, _stage_dir, _path, _content) =
         match crate::chat::lookup::find_story_by_number(project_root, story_number) {
             Some(found) => found,
             None => {
@@ -43,15 +43,8 @@ pub(crate) fn unblock_by_number(project_root: &Path, story_number: &str) -> Stri
             }
         };
 
-    // Prefer DB-backed unblock when the story is in the content store.
-    // Note: `content` may have come from the filesystem fallback in
-    // `find_story_by_number`, so we must re-check the DB rather than
-    // relying on `content.is_some()` alone.
-    if crate::db::read_content(&story_id).is_some() {
-        unblock_by_story_id(&story_id)
-    } else {
-        unblock_by_path(&path, &story_id)
-    }
+    // All state lives in the content store + CRDT now.
+    unblock_by_story_id(&story_id)
 }
 
 /// Unblock a story using the content store (DB-backed).
@@ -99,58 +92,6 @@ fn unblock_by_story_id(story_id: &str) -> String {
     format!("Unblocked **{story_name}** ({story_id}). Cleared: {}. Retry count reset to 0.", cleared.join(", "))
 }
 
-/// Core unblock logic: reset blocked state for a known story file path.
-///
-/// Reads front matter, verifies the story is blocked, clears the `blocked`
-/// flag, and resets `retry_count` to 0.  Also used by the MCP `unblock` tool
-/// when the caller has already resolved the story path from a full `story_id`.
-pub(crate) fn unblock_by_path(path: &Path, story_id: &str) -> String {
-    let contents = match std::fs::read_to_string(path) {
-        Ok(c) => c,
-        Err(e) => return format!("Failed to read story file: {e}"),
-    };
-
-    let meta = match parse_front_matter(&contents) {
-        Ok(m) => m,
-        Err(e) => return format!("Failed to parse front matter for **{story_id}**: {e}"),
-    };
-
-    let story_name = meta.name.as_deref().unwrap_or(story_id).to_string();
-
-    let has_blocked = meta.blocked == Some(true);
-    let has_merge_failure = meta.merge_failure.is_some();
-
-    if !has_blocked && !has_merge_failure {
-        return format!(
-            "**{story_name}** ({story_id}) is not blocked. Nothing to unblock."
-        );
-    }
-
-    // Clear the blocked flag if present.
-    if has_blocked && let Err(e) = clear_front_matter_field(path, "blocked") {
-        return format!("Failed to clear blocked flag on **{story_id}**: {e}");
-    }
-
-    // Clear merge_failure if present.
-    if has_merge_failure && let Err(e) = clear_front_matter_field(path, "merge_failure") {
-        return format!("Failed to clear merge_failure on **{story_id}**: {e}");
-    }
-
-    // Reset retry_count to 0 (re-read the updated file, modify, write).
-    let updated_contents = match std::fs::read_to_string(path) {
-        Ok(c) => c,
-        Err(e) => return format!("Failed to re-read story file after unblocking: {e}"),
-    };
-    let with_retry_reset = set_front_matter_field(&updated_contents, "retry_count", "0");
-    if let Err(e) = std::fs::write(path, &with_retry_reset) {
-        return format!("Failed to reset retry_count on **{story_id}**: {e}");
-    }
-
-    let mut cleared = Vec::new();
-    if has_blocked { cleared.push("blocked"); }
-    if has_merge_failure { cleared.push("merge_failure"); }
-    format!("Unblocked **{story_name}** ({story_id}). Cleared: {}. Retry count reset to 0.", cleared.join(", "))
-}
 
 // ---------------------------------------------------------------------------
 // Tests
diff --git a/server/src/crdt_state.rs b/server/src/crdt_state.rs
index 8d2e97f8..a76db4d0 100644
--- a/server/src/crdt_state.rs
+++ b/server/src/crdt_state.rs
@@ -3,7 +3,7 @@
 /// The CRDT document is the primary source of truth for pipeline item
 /// metadata (stage, name, agent, etc.).  CRDT ops are persisted to SQLite so
 /// state survives restarts.  The filesystem `.huskies/work/` directories are
-/// still updated as a secondary output for backwards compatibility.
+/// no longer written to — all state lives in the CRDT and DB content store.
 ///
 /// Stage transitions detected by `write_item()` are broadcast as [`CrdtEvent`]s
 /// so subscribers (auto-assign, WebSocket, notifications) can react without
diff --git a/server/src/db/mod.rs b/server/src/db/mod.rs
index 53a7664d..b4786b36 100644
--- a/server/src/db/mod.rs
+++ b/server/src/db/mod.rs
@@ -404,6 +404,78 @@ pub fn next_item_number() -> u32 {
     max_num + 1
 }
 
+/// One-time migration: sync CRDT stages from the pipeline_items DB table.
+///
+/// During the filesystem→CRDT migration, many stories were imported into the
+/// CRDT with stage `1_backlog` but then moved forward (to done/archived) via
+/// filesystem-only moves that never wrote CRDT ops.  This leaves stale
+/// `1_backlog` entries in the CRDT for stories that are actually done.
+///
+/// This function reads the authoritative stage from `pipeline_items` and
+/// calls `write_item` to correct any CRDT entries that disagree.
+#[cfg(test)]
+pub async fn sync_crdt_stages_from_db(db_path: &Path) {
+    slog!("[db-sync] START: sync_crdt_stages_from_db called with {}", db_path.display());
+
+    let options = SqliteConnectOptions::new().filename(db_path);
+    let Ok(pool) = SqlitePool::connect_with(options).await else {
+        slog!("[db-sync] FAIL: could not connect to pipeline.db");
+        return;
+    };
+
+    type SyncRow = (String, String, Option<String>, Option<String>, Option<i64>, Option<bool>, Option<String>);
+    let rows: Vec<SyncRow> =
+        sqlx::query_as(
+            "SELECT id, stage, name, agent, retry_count, blocked, depends_on FROM pipeline_items"
+        )
+        .fetch_all(&pool)
+        .await
+        .unwrap_or_default();
+
+    slog!("[db-sync] loaded {} rows from pipeline_items", rows.len());
+
+    let mut corrected = 0u32;
+    let mut skipped = 0u32;
+    let mut first_few = 0u32;
+    for (story_id, db_stage, name, agent, retry_count, blocked, depends_on) in &rows {
+        let crdt_stage = crate::crdt_state::read_item(story_id)
+            .map(|v| v.stage.clone());
+
+        if first_few < 5 {
+            slog!("[db-sync] sample: '{story_id}' crdt={crdt_stage:?} db={db_stage}");
+            first_few += 1;
+        }
+
+        // Skip stale "deleted" shadow rows left by old code that used the
+        // "deleted" sentinel as a soft-delete instead of issuing a real SQL
+        // DELETE.  Syncing these back into the CRDT would resurrect tombstoned
+        // items with stage = "deleted".
+        if db_stage == "deleted" {
+            skipped += 1;
+            continue;
+        }
+
+        if crdt_stage.as_deref() != Some(db_stage.as_str()) {
+            crate::crdt_state::write_item(
+                story_id,
+                db_stage,
+                name.as_deref(),
+                agent.as_deref(),
+                *retry_count,
+                *blocked,
+                depends_on.as_deref(),
+                None,
+                None,
+                None, // merged_at unknown for migrated items; epoch fallback sweeps them
+            );
+            corrected += 1;
+        } else {
+            skipped += 1;
+        }
+    }
+
+    slog!("[db-sync] DONE: corrected={corrected} skipped={skipped} total={}", rows.len());
+}
 
 #[cfg(test)]
 mod tests {
diff --git a/server/src/http/mcp/merge_tools.rs b/server/src/http/mcp/merge_tools.rs
index 54fa7ef0..b7786803 100644
--- a/server/src/http/mcp/merge_tools.rs
+++ b/server/src/http/mcp/merge_tools.rs
@@ -1,6 +1,6 @@
 use crate::agents::move_story_to_merge;
 use crate::http::context::AppContext;
-use crate::io::story_metadata::write_merge_failure;
+use crate::io::story_metadata::write_merge_failure_in_content;
 use crate::slog;
 use crate::slog_warn;
 use serde_json::{json, Value};
@@ -134,26 +134,16 @@ pub(super) fn tool_report_merge_failure(args: &Value, ctx: &AppContext) -> Resul
         reason: reason.to_string(),
     });
 
-    // Persist the failure reason to the story file's front matter so it
+    // Persist the failure reason to the content store + CRDT so it
     // survives server restarts and is visible in the web UI.
-    if let Ok(project_root) = ctx.state.get_project_root() {
-        let story_file = project_root
-            .join(".huskies")
-            .join("work")
-            .join("4_merge")
-            .join(format!("{story_id}.md"));
-        if story_file.exists() {
-            if let Err(e) = write_merge_failure(&story_file, reason) {
-                slog_warn!(
-                    "[mergemaster] Failed to persist merge_failure to story file for '{story_id}': {e}"
-                );
-            }
-        } else {
-            slog_warn!(
-                "[mergemaster] Story file not found in 4_merge/ for '{story_id}'; \
-                 merge_failure not persisted to front matter"
-            );
-        }
+    if let Some(contents) = crate::db::read_content(story_id) {
+        let updated = write_merge_failure_in_content(&contents, reason);
+        crate::db::write_item_with_content(story_id, "4_merge", &updated);
+    } else {
+        slog_warn!(
+            "[mergemaster] No content in store for '{story_id}'; \
+             merge_failure not persisted"
+        );
     }
 
     Ok(format!(
diff --git a/server/src/http/mcp/qa_tools.rs b/server/src/http/mcp/qa_tools.rs
index dc675151..8af17a12 100644
--- a/server/src/http/mcp/qa_tools.rs
+++ b/server/src/http/mcp/qa_tools.rs
@@ -46,12 +46,10 @@ pub(super) async fn tool_approve_qa(args: &Value, ctx: &AppContext) -> Result<St
 
     let project_root = ctx.agents.get_project_root(&ctx.state)?;
 
-    // Clear review_hold before moving
-    let qa_path = project_root
-        .join(".huskies/work/3_qa")
-        .join(format!("{story_id}.md"));
-    if qa_path.exists() {
-        let _ = crate::io::story_metadata::clear_front_matter_field(&qa_path, "review_hold");
+    // Clear review_hold in content store + CRDT before moving.
+    if let Some(contents) = crate::db::read_content(story_id) {
+        let updated = crate::io::story_metadata::clear_front_matter_field_in_content(&contents, "review_hold");
+        crate::db::write_item_with_content(story_id, "3_qa", &updated);
     }
 
     // Move story from work/3_qa/ to work/4_merge/
diff --git a/server/src/io/story_metadata.rs b/server/src/io/story_metadata.rs
index 55a6deda..8becd083 100644
--- a/server/src/io/story_metadata.rs
+++ b/server/src/io/story_metadata.rs
@@ -133,25 +133,10 @@ fn build_metadata(front: FrontMatter) -> StoryMetadata {
 
 /// Write or update a `merge_failure:` field in the YAML front matter of a story file.
 ///
-/// The reason is stored as a quoted YAML string so that colons, hashes, and newlines
-/// in the failure message do not break front-matter parsing.
-/// If no front matter is present, this is a no-op (returns Ok).
-pub fn write_merge_failure(path: &Path, reason: &str) -> Result<(), String> {
-    let contents =
-        fs::read_to_string(path).map_err(|e| format!("Failed to read story file: {e}"))?;
-
-    // Produce a YAML-safe inline quoted string: collapse newlines, escape inner quotes.
-    let escaped = reason.replace('"', "\\\"").replace('\n', " ").replace('\r', "");
-    let yaml_value = format!("\"{escaped}\"");
-
-    let updated = set_front_matter_field(&contents, "merge_failure", &yaml_value);
-    fs::write(path, &updated).map_err(|e| format!("Failed to write story file: {e}"))?;
-    Ok(())
-}
-
 /// Write `review_hold: true` to the YAML front matter of a story file.
 ///
 /// Used to mark spikes that have passed QA and are waiting for human review.
+#[cfg(test)]
 pub fn write_review_hold(path: &Path) -> Result<(), String> {
     let contents =
         fs::read_to_string(path).map_err(|e| format!("Failed to read story file: {e}"))?;
@@ -164,6 +149,7 @@ pub fn write_review_hold(path: &Path) -> Result<(), String> {
 ///
 /// If front matter is present and contains the key, the line is removed.
 /// If no front matter or key is not found, the file is left unchanged.
+#[cfg(test)]
 pub fn clear_front_matter_field(path: &Path, key: &str) -> Result<(), String> {
     let contents =
         fs::read_to_string(path).map_err(|e| format!("Failed to read story file: {e}"))?;
@@ -241,23 +227,12 @@ pub fn set_front_matter_field(contents: &str, key: &str, value: &str) -> String
     result
 }
 
-/// Write `blocked: true` to the YAML front matter of a story file.
-///
-/// Used to mark stories that have exceeded the retry limit and should not
-/// be auto-assigned again.
-pub fn write_blocked(path: &Path) -> Result<(), String> {
-    let contents =
-        fs::read_to_string(path).map_err(|e| format!("Failed to read story file: {e}"))?;
-    let updated = set_front_matter_field(&contents, "blocked", "true");
-    fs::write(path, &updated).map_err(|e| format!("Failed to write story file: {e}"))?;
-    Ok(())
-}
-
 /// Write or update a `depends_on:` field in the YAML front matter of a story file.
 ///
 /// Serialises `deps` as an inline YAML sequence, e.g. `[477, 478]`.
 /// If `deps` is empty the field is removed.
 /// If no front matter is present, this is a no-op (returns Ok).
+#[cfg(test)]
 pub fn write_depends_on(path: &Path, deps: &[u32]) -> Result<(), String> {
     let contents =
         fs::read_to_string(path).map_err(|e| format!("Failed to read story file: {e}"))?;