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If it's helpful, here's some history on Save and save_as in configdialog.
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Item: Code change which added the lines to always save 'highlight' and 'keys'.
November 16, 2004, commit 5acdf9308191b6356fb3ed4ba691ba5cd391f202
commit message:
 Saving a Keyset w/o making changes (by using the "Save as New Custom ...
...Key Set"
button) caused IDLE to fail on restart (no new keyset was created in
config-keys.cfg). Also true for Theme/highlights. Python Bug 1064535.
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Item: Code change to always save 'main' first. Not much information, but seems to be part of the handling of the help source changes.
March 26, 2002 commit 0c5bc8c9518fd18d41aedede536c4a9aa8dfa619 
Commit message: further work on new config system;
user defined help items
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