fix(artifacts): stale data on prompt chunking transitions + query list regression

Two bugs from the artifacts-in-datomic refactor:

1. save-prompt! didn't retract the old storage format when switching
   between chunked and non-chunked templates. A small→chunked save
   left the old :artifact.prompt/template value, which load-prompt
   would return instead of the new chunks. Fixed by always retracting
   old chunks and clearing the template string when switching formats.

2. do-query wrapped `query list` inside with-existing-db, requiring
   a repo path for a command that only needs the meta database.
   Moved list-queries handling back outside the repo-dependent path.

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

Author: leifericf

src/noumenon/artifacts.clj

@@ -157,13 +157,27 @@
 ;; --- Writing ---
 
 (defn save-prompt!
-  "Write a prompt template to Datomic. Handles chunking transparently."
+  "Write a prompt template to Datomic. Handles chunking transparently.
+   Retracts the opposite storage format to prevent stale data."
   [conn prompt-name template source]
-  (let [tx-data (merge {:artifact.prompt/name prompt-name}
-                       (chunk-template template))]
-    (d/transact conn {:tx-data [tx-data
-                                {:db/id "datomic.tx"
-                                 :tx/artifact-source source}]})))
+  (let [db       (d/db conn)
+        entity   (d/pull db '[:db/id :artifact.prompt/template
+                              {:artifact.prompt/chunks [:db/id]}]
+                         [:artifact.prompt/name prompt-name])
+        eid      (:db/id entity)
+        chunked? (> (count template) chunk-size)
+        ;; Retract stale data: old template string and/or old chunks
+        retracts (when eid
+                   (into (when (and chunked? (:artifact.prompt/template entity))
+                           [[:db/retract eid :artifact.prompt/template
+                             (:artifact.prompt/template entity)]])
+                         (map (fn [chunk] [:db/retractEntity (:db/id chunk)]))
+                         (:artifact.prompt/chunks entity)))
+        tx-data  (merge {:artifact.prompt/name prompt-name}
+                        (chunk-template template))]
+    (d/transact conn {:tx-data (into [tx-data {:db/id "datomic.tx"
+                                               :tx/artifact-source source}]
+                                     retracts)})))
 
 (defn save-rules!
   "Write rules to Datomic."

src/noumenon/main.clj

@@ -247,14 +247,15 @@
 (defn do-query
   "Run the query subcommand. Returns {:exit n :result map-or-nil}."
   [{:keys [query-name list-queries params] :as opts}]
-  (with-valid-repo
-    opts
-    (fn [ctx]
-      (with-existing-db
-        ctx
-        (fn [{:keys [db meta-db]}]
-          (if list-queries
-            (do-query-list meta-db)
+  (if list-queries
+    (let [meta-conn (db/ensure-meta-db (util/resolve-db-dir opts))]
+      (do-query-list (d/db meta-conn)))
+    (with-valid-repo
+      opts
+      (fn [ctx]
+        (with-existing-db
+          ctx
+          (fn [{:keys [db meta-db]}]
             (let [kw-params (into {} (map (fn [[k v]] [(keyword k) v])) params)
                   {:keys [ok error]} (query/run-named-query meta-db db query-name kw-params)]
               (if error