Develop Reference

Android Studio GIT error when trying to annotate

When I right click on the side and click "Annotate" I get the following error
Error:Failed to annotate: com.intellij.openapi.vcs.VcsException:
fatal: no such path app/src/main/java/.. ../MainActivity.java in HEAD
during executing git -c core.quotepath=false blame --porcelain -l -t
-w HEAD -- app/src/main/java/.. ../MainActivity.java
Google didnt help. I tried cloning the repo again but didnt work. I have no idea whats going on.
Also when I try to look at the history, the console says something like
fatal: no such path .../MainActivity.java in HEAD

I struggled for months with this happening but just for Git submodule code - and in my case the "Oh you renamed your folders" solutions didn't help me at all.
Finally this was the solution for my case:
Go to Android Studio Preferences, Version Control tab
Under the Directory list, add in all the submodule root folders (you may find they are already there but under an "Unregistered" header in the list - in that case you can simply select those and hit the + button, bottom left, to add them.)
That's it, fixed my annotate and git change highlighting issues.

The OP got it resolved now, but I am answering this for who came across this problem like I just did.
The paths in git repo are case-sensitive. So try to rename your folder in git to match the checkout folder on your system, especially if you are on Mac/Linux. Try run annotate again should work now.
git mv FOO foo2
git mv foo2 foo
git commit -m "Fix case sensitivity"

Getting "detached HEAD" error despite deleting git submodule

Git seems to be tracking the java folder, but I can't commit changes to the specific file MainActivity.java. I get a "Changes not staged for commit"
The diff shows the changes, but I can't commit it.
Also, I can't go down into the folder in Github.
That folder is not clickable.
Edit: When I do git status in the command line, I get
user:JustJava juil$ git status
HEAD detached at 93ea9a1
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git checkout -- <file>..." to discard changes in working directory)
(commit or discard the untracked or modified content in submodules)
modified: app/src/main/java/com/example/android/justjava (modified content)
no changes added to commit (use "git add" and/or "git commit -a")
Edit 2: I have checked out the latest commit as some have suggested but still get the detached head error.
Edit 3: I tried adding the file itself w/ git add but got an error that the directory is a submodule.
JustJava juil$ git add app/src/main/java/com/example/android/justjava/MainActivity.java
fatal: Pathspec 'app/src/main/java/com/example/android/justjava/MainActivity.java' is in submodule 'app/src/main/java/com/example/android/justjava'
I tried running git submodule status and got the error
fatal: no submodule mapping found in .gitmodules for path 'app/src/main/java/com/example/android/justjava'
I tried deleting .git in the submodule, but the same error keeps popping up.

To correct this using just the Android Studio interface, try the following:
Make a backup copy of your changed files, just in case this method doesn't merge your changes correctly.
In the version control pane, select the Log tab. It will show you a list of commits.
The top commit should be the newest one. Right click it and select Checkout Revision in the context menu.
If a dialog appears, select Smart Checkout. This will merge your changes with the selected commit.
Your HEAD should now be attached, so you can commit normally now.

When your HEAD is detached, it means you did the commandline equivalent of:
git checkout <UUID of previous commit>
The grey folder that was created is called a submodule, it happens when you initialize a git repository inside another git repository. I would suggest removing the .git folder inside JustJava/app/src/main/java/com/example/android/justjava.
Using git through terminal, follow these steps:
Backup all the code in a different folder
**Remove JustJava/app/src/main/java/com/example/android/justjava/.git"
Checkout out master or the current branch you're on (default: master)
In order to checkout master, go to the folder where you git project is through the terminal (linux or mac) or git bash (if you're on windows), then do:
git checkout master
Comparing backed up code with the current code and make the changes you want (if any)
Commit new code

Since justjava folder turned out to be a submodule, in the super directory, I called git rm -rf --cached justjava as suggested by #fusiongate and answered in this question.
This works in that it allows the file to be added and committed, but the commit history on this file is lost.

Removing build folder from git

I have pushed a build folder to my remote repo; but the .gitignore file clearly has this line (/payu_ui/build); But i found out since the build files were already tracked once and now that i wrote a line in .gitignore will not really ignore the build folder. So i want to remove it from git from being tracked (the complete build folder) so i used this command
git filter-branch --index-filter 'git rm -r --cached --ignore-unmatch payu_ui/build/' --prune-empty --tag-name-filter cat -- --all
But every time i run this command it gives an err saying
fatal: bad revision 'rm'
So what is going wrong; every time i click the commit option from IDE it shows that 1300 files needs to be committed (its annoying me)
Any help will be appreciated;
1. I dont want to track these build files(from payu_ui lib)
2. I dont want to push them to remote repo (but its already thr and beleive once i track from local and push them it gets deleted in remote repo; if it doesn't i'll manually delete in remote repo)

Well you may just do the following,
Remove the line from gitignore for now.
Locally delete the folder.
Push out the change so the folder gets deleted from remote as well.
Now add the line to gitignore.
I recently faced the problem and that is what i did.

remove those build files (or whole folder) from your computer
rm -r [direction to files]
then add, commit and push all your changes (actually the change will be removing those files from repository), if you have set .gitignore
file properly, git will stop tracking those files

Android Studio .iml git issue

When I try to make a "git pull" I get the following message :
error: The following untracked working tree files would be overwritten by merge:
blablabla.iml
Please move or remove them before you can merge.
Aborting
I try to checkout the .iml and add it to my gitignore but I keep receiving this message. Does someone know how to fix it?
Regards
Jose

Git will not allow you to execute a pull that would cause you to lose changes in your working directory (this is good for obvious reasons).
Adding the file to your .gitignore will tell git not to push your changes to that file to other repositories, but it does not prevent you from pulling other repositories changes of those files. So this actually has no effect on the operation you are trying to do. As a side note, it is not recommended to put iml files in a .gitignore: What should be in my .gitignore for an Android Studio project?.
Here's what I would do:
Stash your local changes: git stash save "My iml changes"
Then checkout the code: git pull
Optionally, get your local changes out of the stash: git stash pop. Or, if you prefer, git stash drop stash#{0} (As pointed out by #LoyalRayne, you might not need these changes). See the differences with git stash show stash#{0}.

If you want the contents that are currently in the repo, you can revert your local changes first with git checkout blablabla.iml, then pull. Or, if you want to keep your local changes, do git stash, then git pull, then git apply.
After doing the above steps, you may add the file to .gitignore. Make sure to remove it from source control as well with git rm --cached blablabla.iml. Note that when it is remove from source control, it will get deleted on other people's machines when they do their next git pull, so they will want to create a backup.

error syncing with cyanogenmod repo

I have followed the instructions here to get the cynogenmod source on my system.
i was able to do the build successfully. I didn't do any local source changes. Now when i try to get the latest source using repo sync command, I am getting the following errors
error: Your local changes to the following files would be overwritten by checkout:
Android.mk
extendedcommands.c
flashutils/Android.mk
flashutils/flashutils.c
flashutils/flashutils.h
mounts.c
mounts.h
nandroid.c
roots.c
Please, commit your changes or stash them before you can switch branches.
Aborting
error: Your local changes to the following files would be overwritten by checkout:
encore.mk
init.encore.rc
Please, commit your changes or stash them before you can switch branches.
Aborting
<few more errors like this.........>
error: bootable/recovery/: CyanogenMod/android_bootable_recovery checkout 50822991460cbee65757e9de12b29e39238d6386
error: device/bn/encore/: CyanogenMod/android_device_bn_encore checkout f6586ab41f0e3f5acfa16b43f9b17008e9bb0524
I have tried repo forall -c git reset --hard HEAD without success.
Any suggestions on how i can resolve these errors?

Apparently I was facing this issue because I had the repository on an NTFS partition. NTFS was not storing the permissions on the file properly and Git was seeing that as a change.
You can force Git to ignore the permissions on the file while looking for changes by using the following command:
repo forall -c git config core.filemode false
(Not sure if this has any side effect. If there is, please let me know!)