Can you go to Preferences > Files > Extensions, and press the "Register Filetypes" button to register the extensions again? You may need to restart the PC before this takes effect.
You can go to Preferences > Program Window and enable the "Ignore unrecognized PL/SQL" option. This way SQL*Plus commands like "SHOW ERRORS" will be ignored.
Using *.sql for everything including SQL scripts and PL/SQL source code is a terrible idea. They do it on my current project but it turns out they don't need to (the deployment script we use used to have a limitation, but it doesn't any more) and it's only a convention. Maybe you can get it changed. Java developers would never let themselves be forced to use .java for all Java-related files.
I was trying to make one tool script, is it possible to past parameter #dir or #path with windows path not PL/SQL internal which gives \INTERF~1\. For cvs history diff I need full windows path.