Some tweaks to merge

Adds note about behavior, some edge case handling around other flags that might start with --file, permissions issues, etc.

refresh.template.py

@@ -1065,16 +1065,17 @@ def _ensure_cwd_is_workspace_root():
     for (target, flags) in target_flag_pairs:
         compile_command_entries.extend(_get_commands(target, flags))
 
-    should_merge = any(arg.startswith('--file') for arg in sys.argv[1:])
-    if should_merge and os.path.isfile('compile_commands.json'):
-        origin_compile_command_entries = []
-        with open('compile_commands.json') as fd:
-            try:
-                origin_compile_command_entries = json.load(fd)
-            except:
-                log_warning(">>> Failed to merge compile_commands.json the file seems has broken")
-        files_index = set(entry['file'] for entry in compile_command_entries)
-        compile_command_entries += [entry for entry in origin_compile_command_entries if entry['file'] not in files_index]
+    # --file triggers incremental update of compile_commands.json
+    if any(arg.startswith('--file=') for arg in sys.argv[1:]) and os.path.isfile('compile_commands.json'):
+        previous_compile_command_entries = []
+        try:
+            with open('compile_commands.json') as compile_commands_file:
+                previous_compile_command_entries = json.load(compile_commands_file)
+        except:
+            log_warning(">>> Couldn't read previous compile_commands.json. Overwriting instead of merging...")
+        else:
+            updated_files = set(entry['file'] for entry in compile_command_entries)
+            compile_command_entries += [entry for entry in previous_compile_command_entries if entry['file'] not in updated_files]
 
     # Chain output into compile_commands.json
     with open('compile_commands.json', 'w') as output_file: