A common task for a developer has is to apply a patch in Git. I have a simple scheme that I've been using for a long time and it is very seldom that I get into problem nowadays when I'm doing patch work.
The short version for the impatient
$ git am < my_new_feature.patch
$ git apply --reject --whitespace=fix my_new_feature.patch
$ git status
$ vim my_conflicting_file.c*
$ find . -name "*.rej" -exec rm -f {} \;
$ git add .
$ git am --resolved
Long version for the one needing explanations to the steps
To start with I always first try applying the patch with git am, i.e.
$ git am < my_new_feature.patch
Sometimes this is enough and the patch simply applies, however when it fails to apply I just continue writing.
$ git apply --reject --whitespace=fix my_new_feature.patch
This will force Git to apply as much as it can and for the rest of the hunks that it cannot merge it will produce files ending with .rej. So the next step I do after git apply is just to run
$ git status
And notice the untracked files ending in .rej. Now I know what files Git couldn't merge when applying the patch, so let's say that I have a file called my_conflicting_file.c which Git couldn't merge. To solve this I open it in my favorite editor by doing like this:
$ vim my_conflicting_file.c*
This will open both my_conflicting_file.c and my_conflicting_file.c.rej. I will split the window in vim (CTRL+W V), and then open the other file by typing :bp in vim. Now it is up to you as a developer to decicde what changes in the .rej file should go into the conflicting file. I.e, what changes in my_conflicting_file.c.rej, should be in my_conflicting_file.c. Sometimes you will notice that you don't have to change anything at all and sometimes you will notice that you have to add or remove lines in the conflicting file. Don't forget to remove the + and/or - at the start of the lines in the .rej file! When this step is done I delete all the *.rej files and then add the changes files to the index in Git. I.e:
$ find . -name "*.rej" -exec rm -f {} \;
$ git add .
The last step you have to do before the patch have been merged is to tell git that the "am" that you started have been resolved.
$ git am --resolved
Patch work done! If you follow this scheme I'm pretty sure that you will do fine in the future when applying patches.