git clone PATH DIR
git pull --rebase
... work work work ...
git pull --rebase
... fix conflicts ...
git push

Note: using --rebase is controversial, as it discards all the change information in the local repository, lumping all your local changes as if they'd just been made to the contents of the remote repository.

When git pull says "Cannot merge": 

git checkout -m -b temporary_branch
git commit -a
git merge origin master
#resolve conflicts
git commit -a

or something like that 

Only run git add on new files just before committing. Otherwise, you'll commit the wrong contents of the file.
....
The only way around it is to start using the index more. For example, when you have to commit only some of the changes in the working tree, or when you are adding new files to the tree, you could not use the command line tools. Instead, fire git citool which is a graphical user interface to examine changes, stage them, and finally commit them. It is powerful, easy to use, and will provide a gentle introduction to the concept of a staging area. It also will catch mistakes such as the above one.

Here is how you go solving conflicts after git pull --rebase has failed:

    * git diff will show you changes in the conflicted files;
    * since git add will stop showing a file in git diff (until you change it again), you can use it to mark a file as resolved;
    * at the end, your git diff should be empty, since you should have resolved the conflicts;
    * now, use git commit (without -a) to commit the result of the merge. Why no -a? Because the result of the merge is already in the index; and without any parameters, git commit transforms the index into a commit.

    * git diff shows you the differences from index to working tree
    * git diff HEAD shows you the differences from trunk to working tree
    * git diff --cached shows you the differences from trunk to index

 git status has output that is very different from svn status, but the latter can be very useful. Luckily, you can obtain subversion-like output with the invocation git diff --name-status -r; since this is quite a mouthful, you can add this to your ~/.gitconfig file:

[alias]
       changes=diff --name-status -r

You have now created a git changes command that knows about all of git diff's option. In particular the three invocations git changes, git changes HEAD, or git changes --cached, will have the same meaning as the git diff commands above.

Since you are at it, add this to ~/.gitconfig too:

[diff]
       renames = true

and also tell git about your identity like this:

[user]
       name = Paolo Bonzini
       email = bonzini@gnu.org

The name and e-mail address will be used to identify you in commits.

If you ever want to overwrite any of your local modifications, you can do another checkout with the -f option to bring you back to a clean slate:

$ git-checkout -f

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