Moved plugins and refactor command system

- Moved plugins to apropriate sub folders
- Refactor command system with new add_command method and rename GetCommandSystemEvent to GetNewCommandSystemEvent
- Add RegisterCommandEvent for dynamic command registration
- Change footer container orientation to VERTICAL
- Add search-highlight tag to source buffer
- Add file change detection (deleted, externally modified) in source_file
- Add JSON prettify option to source view popup menu
- Enable hexpand on VTE widget
- Update plugins_controller_mixin to use widget_registry

plugins/code/search_replace/mixins/replace_mixin.py

@@ -0,0 +1,50 @@
+# Python imports
+
+# Lib imports
+
+# Application imports
+
+
+
+class ReplaceMixin:
+
+    def _replace_word(
+        self,
+        current_index: int,
+        to_text: str,
+        buffer: any
+    ):
+        self.clear_highlight(buffer)
+
+        start_itr, end_itr = self.matches[current_index]
+        self.active_view.scroll_to_iter(end_itr, 0.2, False, 0, 0)
+
+        buffer.begin_user_action()
+        buffer.delete(start_itr, end_itr)
+        buffer.insert(start_itr, to_text)
+        buffer.end_user_action()
+
+    def _replace_all_words(self, to_text: str, buffer: any):
+        marks: list = []
+
+        for start_itr, end_itr in self.matches:
+            start_mark = buffer.create_mark(None, start_itr, left_gravity = True)
+            end_mark   = buffer.create_mark(None, end_itr, left_gravity = False)
+            marks.append((start_mark, end_mark))
+
+        buffer.begin_user_action()
+
+        for start_mark, end_mark in reversed(marks):
+            start_itr = buffer.get_iter_at_mark(start_mark)
+            end_itr   = buffer.get_iter_at_mark(end_mark)
+
+            buffer.delete(start_itr, end_itr)
+            buffer.insert(start_itr, to_text)
+
+        buffer.end_user_action()
+
+        for start_mark, end_mark in marks:
+            buffer.delete_mark(start_mark)
+            buffer.delete_mark(end_mark)
+
+        self.find_entry.grab_focus()