The LLVM source is stored in the llvm/ directory. To update the LLVM to the latest git version:

git fetch llvm_remote
git checkout llvm_branch
git merge llvm_remote/master
git checkout master
git merge --squash -X subtree=llvm --no-commit llvm_branch

This is how I setup my local repository to have a branch of LLVM mainline:

git remote add llvm_remote http://llvm.org/git/llvm.git
git fetch llvm_remote
git checkout -b llvm_branch llvm_remote/master
git checkout master
git read-tree --prefix=llvm/ -u llvm_branch

Same as above but from repository:

http://llvm.org/git/polly.git

Reading in the tree:

git read-tree --prefix=llvm/tools/polly/ -u polly_branch

Same as above but from repository:

git://repo.or.cz/cloog.git

Reading in the tree:

git read-tree --prefix=cloog/ -u cloog_branch

Same as above but from repository:

git://repo.or.cz/isl.git

Reading in the tree:

git read-tree --prefix=cloog/isl -u isl_branch

Note: Don't forget to run this after updating cloog and isl:

./autogen.sh