Reorganize top-level directories with clearer naming convention

app -> app-desktop-macos, presets -> app-presets, server -> remote-server,
daw-config-reaper -> osc-config-daw, plugin-reaper-realearn -> plugin-reaper-relearn.
Updated run.py and presets.py path references accordingly.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

plugin-reaper-relearn/regenerate-doc-diagrams.sh

@@ -0,0 +1,15 @@
+#!/bin/sh
+# This regenerates the D2 diagrams in the Antora documentations (requires d2 executable in path)
+process_files() {
+  local DIR="$1"
+  for FILE in "$DIR"/*.d2; do
+    if [ -f "$FILE" ]; then
+      FILE_NAME=$(basename "$FILE")
+      echo "Processing $FILE_NAME"
+      FILE_NAME_NO_EXT="${FILE_NAME%.*}"
+      d2 --sketch "$FILE" "$DIR/target/$FILE_NAME_NO_EXT.svg"
+    fi
+  done
+}
+
+process_files "doc/realearn/modules/ROOT/images/realearn/diagrams/control-flow"