feat(1001): recover_half_written_items MCP tool

Adds db::recover, a discovery + recovery layer for pipeline items that
got half-written before the Stage 1 fix landed (content in content
store + SQLite shadow, no live CRDT entry). For each orphan, the
content body is re-anchored to a fresh non-tombstoned id and the old
id's content row is cleared.

Exposed as the recover_half_written_items MCP tool. dry_run defaults
to true so the caller can review what would change before mutating.

YAML front-matter parsing is hand-rolled and scoped to the three
fields the create_*_file path emits (name, type, depends_on). It
tolerates missing or malformed lines by falling back to safe
defaults; the orphan is recovered with the best metadata we can pull
from the body and the rest is left to the operator to fix up.

The discovery step is read-only and idempotent. Recovery is also
idempotent in the sense that once an orphan is lifted, the next
discovery pass won't see it.

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

server/src/http/mcp/diagnostics/mod.rs

@@ -115,6 +115,46 @@ pub(crate) fn tool_dump_crdt(args: &Value) -> Result<String, String> {
     .map_err(|e| format!("Serialization error: {e}"))
 }
 
+/// MCP tool: discover or recover half-written pipeline items (bug 1001).
+///
+/// A half-written item is one whose content row is in the content store /
+/// SQLite shadow but whose CRDT entry is absent or tombstoned.  Such items
+/// are invisible to every CRDT-driven read path and to `delete_story` /
+/// `purge_story`, so they need explicit recovery.
+///
+/// With `dry_run = true` (default), returns the list of discovered half-
+/// writes without mutating anything.  With `dry_run = false`, lifts each
+/// orphan onto a fresh non-tombstoned id and returns the old→new mapping.
+pub(crate) fn tool_recover_half_written_items(args: &Value) -> Result<String, String> {
+    let dry_run = args
+        .get("dry_run")
+        .and_then(|v| v.as_bool())
+        .unwrap_or(true);
+
+    if dry_run {
+        let half = crate::db::find_half_written_items();
+        return serde_json::to_string_pretty(&json!({
+            "dry_run": true,
+            "found": half,
+            "count": half.len(),
+            "message": format!(
+                "Discovered {} half-written item(s). Re-run with dry_run=false to recover them.",
+                half.len()
+            ),
+        }))
+        .map_err(|e| format!("Serialization error: {e}"));
+    }
+
+    let results = crate::db::recover_half_written_items();
+    serde_json::to_string_pretty(&json!({
+        "dry_run": false,
+        "recovered": results,
+        "count": results.len(),
+        "message": format!("Recovered {} half-written item(s).", results.len()),
+    }))
+    .map_err(|e| format!("Serialization error: {e}"))
+}
+
 /// MCP tool: return the server version, build hash, and running port.
 pub(crate) fn tool_get_version(ctx: &AppContext) -> Result<String, String> {
     let build_hash =