Update Wordpress when using Github Wordpress skeleton - wordpress

Question

This is mainly a clarification about dealing with public Repos for git beginners.
I have a local git repo with a clone of Wordpress skeleton (https://github.com/markjaquith/WordPress-Skeleton). This includes Wordpress as a submodule (https://github.com/WordPress/WordPress).
If I update Wordpress from the dashboard it will require me to update my git repo.
There is a note about making a pull request if the repo falls behind but I am working on my localhost so can't do that.
If I had a hosted repo, should I send a pull request to the WP skeleton or WP repo?
I have a fresh install at the moment but if I were to customise it I probably wont want to (or Shouldn't) push so what would I do in this case?
Note: This is using the Wordpress repo as an example but I am curious about the best/general practice.

Answer 1

I'm having some similar questions, mainly about what the best practice is when updating Wordpress. Should I use the Dashboard once on remote, or should I continue to update the Wordpress Submodule in WP-Skeleton.
I can tell you this, you can update Wordpress via the Submodule in WP-Skeleton by using the "Git Checkout" command on the submodule and choosing the latest release number (4.1 as of this writing). Its extremely simple in SourceTree if you're new to Git and need an interface to help.

Answer 2

This is a little late but I asked the author of the repo and he answered me in his QA repo on Github.
This is the answer Mark Jaquith gave there which worked:
For your personal sites, which have likely wildly diverged, the update
process is as follows:
cd wp
git fetch
git fetch --tags
git checkout 3.9.1
cd ../
git add wp
git commit -m 'Update to WordPress 3.9.1'
git push origin master
Let me break that down:
cd wp — move into the WordPress submodule directory.
git fetch — Pull down the latest changes from tracked branches.
git fetch --tags — Pull down the new tags. You do steps 2 and 3 in this order because otherwise you might have a tag that points to a commit that you don't yet have in your repo.
git checkout 3.9.1 — Checkout the 3.9.1 tag.
cd ../ — Move back into the main directory. At this point, the wp subdirectory will show as having changes, since it points to a different commit.
git add wp — Tell your main repo to stage the WordPress submodule repointing.
git commit -m 'Update to WordPress 3.9.1' — Commit that change git push origin master — Push your master branch (change if using a different branch) up to your origin remote (change if using a different remote).
You probably noticed that there
is only one variable here — the version number. So You could wrap that
up into a bash script that you check into your root directory. And
then you could just do something like: ./wpupdate 3.9.1. Or you could
write a script that iterates through a bunch of WordPress site
checkouts and does this process on each of them (I've done exactly
that).
I will also add that from the wp folder you can enter git tag to see a list of tags, this way you can make sure you get the latest one.