From J.C. Hamano (Git maintainer) himself, this is about:
patch applications and merges in a dirty work tree with a clean index.
- A dirty work tree is where you have changes that are not added to the index.
A work tree that is not dirty is a clean work tree.
- A dirty index is where you have changes already added to it (in other words, "
git diff --cached" will report some changes).
A clean index matches the HEAD.
With recent Git release, you can abort:
To restore the original branch and stop patching run "git am --abort".
Then:
The simplest thing for those who cannot decide may be to stash the changes away for later.
$ git stash save "Random changes that are not ready"
And then redo "git pull" or "git am".
"git stash" is the ultimate tool for people who are afraid of commitment.
After redoing "git pull" or "git am", you can replay the local changes you stashed away:
$ git stash pop
Note: one source of dirty tree can be the autocrlf setting (like in this msysgit issue 81), so make sure to set that to false.
Other source of discrepancy: core.whitespace setting.
The OP mentions in the comment:
Before trying to run git am I did run git stash, so I don't think that was the problem.
What I ended up doing was running git am -3 patch.patch, then manually fixing the problem, then running 'git am --resolved'.
Note: in the recent Git1.7.2 Release Notes:
The message from "git am -3" has been improved when conflict resolution ended up making the patch a no-op.