fix: startup migration syncs stale CRDT stages from pipeline_items DB

510 stories had stale 1_backlog stages in the CRDT because they were
imported during the filesystem→CRDT migration and then moved forward
via filesystem-only moves that never wrote CRDT ops. This made done
stories appear as ghost entries in the backlog.

On startup, reads the authoritative stage from pipeline_items and
corrects any CRDT entries that disagree.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

server/src/db/mod.rs

@@ -341,6 +341,55 @@ 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.
+pub async fn sync_crdt_stages_from_db(db_path: &Path) {
+    let options = SqliteConnectOptions::new().filename(db_path);
+    let Ok(pool) = SqlitePool::connect_with(options).await else {
+        slog!("[db] CRDT stage sync: failed to connect to pipeline.db");
+        return;
+    };
+
+    let rows: Vec<(String, String, Option<String>, Option<String>, Option<i64>, Option<bool>, Option<String>)> =
+        sqlx::query_as(
+            "SELECT id, stage, name, agent, retry_count, blocked, depends_on FROM pipeline_items"
+        )
+        .fetch_all(&pool)
+        .await
+        .unwrap_or_default();
+
+    let mut corrected = 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 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,
+            );
+            corrected += 1;
+        }
+    }
+
+    if corrected > 0 {
+        slog!("[db] CRDT stage sync: corrected {corrected} items from pipeline_items");
+    }
+}
 
 #[cfg(test)]
 mod tests {

server/src/main.rs

@@ -337,6 +337,12 @@ async fn main() -> Result<(), std::io::Error> {
         }
     }
 
+    // One-time fix: sync CRDT stages from pipeline_items DB for stories
+    // that were migrated with stale backlog stages.
+    if let Some(ref db_path) = pipeline_db_path {
+        db::sync_crdt_stages_from_db(db_path).await;
+    }
+
     // (CRDT state layer is initialised above alongside the legacy pipeline.db.)
 
     // Start the CRDT sync rendezvous client if configured in project.toml.