If you have a file that exists in two branches in the same repo, make a change to it without committing, then switch branches the changes carry over, but if you make changes to a file that exists in only one of the repos and try and switch branches Git complains that the file isn't uptodate. The latter behavior seems correct to me.
Changes I make in any branch should not just follow me around as I switch through other branches. It seems not only conceptually broken to me, but also something that make it very easy to accidentally commit changes to an unintended branch if you weren't paying close attention when you switched. I think that the appropriate action is to not allow a user to switch branches whenever there are files that aren't up to date (committing, git-stash, and checkout -m being the obvious, and safe, ways around the blockage).
The documentation *seems* to agree with me and it looks like it was the intent of the code to prevent this too, but it obviously doesn't.
In case my description was a little confusing below is a real world example of what I'm talking about. The last command is what I believe should not be possible:
$ temp krhodes$ mkdir foo $ temp krhodes$ cd foo/ $ foo krhodes$ git --version git version 1.5.4.2.g41ac4 $ foo krhodes$ git init Initialized empty Git repository in .git/ $ foo krhodes$ echo "foo" > foo.txt $ foo krhodes$ git add foo.txt $ foo krhodes$ git commit -a -m " initial commit" Created initial commit 10d7a21: initial commit 1 files changed, 1 insertions(+), 0 deletions(-) create mode 100644 foo.txt $ foo krhodes$ git checkout -b branch_one Switched to a new branch "branch_one" $ foo krhodes$ echo "bar" > bar.txt $ foo krhodes$ git add bar.txt $ foo krhodes$ git commit -a -m "initial branch_one_commit" Created commit 3251c16: initial branch_one_commit 1 files changed, 1 insertions(+), 0 deletions(-) create mode 100644 bar.txt $ foo krhodes$ echo "baz" > bar.txt $ foo krhodes$ git checkout master fatal: Entry 'bar.txt' not uptodate. Cannot merge. $ foo krhodes$ git checkout bar.txt $ foo krhodes$ git checkout master Switched to branch "master" $ foo krhodes$ echo "baz" > foo.txt $ foo krhodes$ git checkout branch_one M foo.txt Switched to branch "branch_one"
------- -masukomi