The problem comes from the fact that stash lumps all the changes to the tracked files together, without separating all the things you've added to the index. If you've done a patch add with git add -p, this can mean a lot of frustration at having to pick through all the changes again once you do git stash pop.
To avoid this frustration, do the following and you'll be able to keep your staged changes over the course of using stash.
1. First, do a stash of only the things you haven't yet staged:
git stash save --keep-index "Un-staged changes"
At this point, if you run git status, you should see all your changes that have been staged still there, but none of the changes NOT staged for commit (except of course for any untracked files).2. Next, stash the staged changes as you normally would:
git stash save "Staged"
3. Now is when you want to do any work you need to while the other changes are stashed. NOTE: If you need to make changes that are based on a file in the "Un-staged changes" stash, you will of course need to pop that stash specifically with git stash pop stash@{1}. But, in order to get the staged changes back, you'll need to do another git stash save to do things in the correct order.
4. To get your changes back, you're going to pop them off the stash in the reverse order. If you haven't stashed any other changes, you can do a simple pop:
git stash pop
Otherwise, you should run:git stash list
and find the correct name of the stash to pop, e.g. stash@{1}.5. All the changes you just popped aren't staged at this point but should be, so go ahead and add all of them to the index with git add file1 file2 ...
6. Finally, run git stash pop one more time to recover the un-staged changes you saved in step 1 and you'll have everything back to the way it was at the beginning.
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