Upon save ( I think ), my emacs is deleting trailing white space. I don't want to commit those changes, only the parts I manually modify. Is there a way to disable that behaviour?
This behaviour is not standard. It is however a very common customization that you might have borrowed somewhere. Look for something like the following in you init file and comment out those lines to get rid of this behaviour (and have Emacs save files as they are, without removing whitespace altogether):
(add-to-list 'write-file-functions 'delete-trailing-whitespace)
or
(add-hook 'before-save-hook 'delete-trailing-whitespace)
This emacswiki page gives tons of advice on handling trailing whitespace.
If you want to delete trailing whitespace only on lines you modify, you could try the ws-trim package
Like suggested in this answer the deleting-trailing-whitespace
hook might have been added to the before-save-hook
hook.
To disable this eval (remove-hook 'before-save-hook 'delete-trailing-whitespace)
(type M-:).
Take a look at ethan-wspace. It will clean up any whitespace that you made dirty yourself. However any incorrect whitespace that was there when you opened the file is left intact. This way you can avoid those messy diffs full of whitespace changes
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