Fix saving unmodified scenes and resources

When `_save_all_scenes` or `save_resource_in_path` was called, they
always saved all the scenes and the resource no matter if they were
modified or not. For example, when `saving before run` option was
checked, it always overwrote the current scene and the default
environment simply by opening and runing the project.

This PR adds checks for unsaved scenes (using the same `unsave` check
others method used) and modified resources (comparing last modified
time and last import time).

Fix #6025.

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