fix: remove most file graph uses in deps

except for graph-parser and publish deps

- Removed most mentions of 'repo' in deps, which cleaned up a lot related
  to export cli and worker
- Removed db-based-graph? checks in deps except for unknown use
  in entity-plus?
- Removing db-based-graph? checks resulted in deleting unused file graph
  code paths e.g. get-pid
- Removed file graph handling in cli list command
- Remove file-based-graph? checks from deps

deps/outliner/src/logseq/outliner/transaction.cljc

@@ -12,8 +12,7 @@
             {:transact-opts {:conn conn} \"Datascript conn\"
              :additional-tx \"Additional tx data that can be bundled together
                               with the body in this macro.\"
-             :persist-op? \"Boolean, store ops into db (sqlite), by default,
-                            its value depends on (config/db-based-graph? repo)\"}
+             :persist-op? \"Boolean, store ops into db (sqlite)\"}
   `Example`:
   (transact! {:conn db-conn}
     (insert-blocks! ...)

deps/outliner/src/logseq/outliner/tree.cljs

@@ -3,7 +3,7 @@
   (:require [datascript.core :as d]
             [datascript.impl.entity :as de]
             [logseq.db :as ldb]
-            [logseq.db.common.property-util :as db-property-util]))
+            [logseq.db.frontend.property :as db-property]))
 
 (defprotocol INode
   (-save [this *txs-state conn opts])
@@ -12,7 +12,7 @@
 (defn- blocks->vec-tree-aux
   [db blocks root]
   (let [root-id (:db/id root)
-        blocks (remove #(db-property-util/shape-block? db %) blocks)
+        blocks (remove #(db-property/shape-block? db %) blocks)
         parent-blocks (group-by #(get-in % [:block/parent :db/id]) blocks) ;; exclude whiteboard shapes
         sort-fn (fn [parent]
                   (when-let [children (get parent-blocks parent)]