Bitbucket broken directories?

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I have an instance of the edX platform set up on an AWS EC2 server. The site can be seen here http://corporateuni.org.

I deployed edX onto that server following these instructions for "Installing edX on a single Ubuntu 12.04 (Precise) server".

My aim is to set up a git repo on Bitbucket so I can modify source code locally and push it to the repo, and then update the repo at the server end.

I initialised a git repo at the source of the edX project on the server and carried out the following commands:

git init
git add -A
git commit -m "Initial commit, changed branding"
git push -u origin master

This seems to complete fine and all the files appear on Bitbucket.

However, some files appear like this (i.e. edx-platform → e01ea885e49b [e01ea885e49b]):

Broken files 1 Broken files 2

I don't understand exactly what Bitbucket is trying to tell me here. Have these files been excluded by git?

There are some .gitignore files distributed throughout the filesystem but when I check git status, the edx-platform file has been included after the git add -A command. When I clone the repo, the directories appear, but are empty.

Before I go ahead and try to remove all of the .gitignore files, I wanted to see if there was another solution to this problem and what exactly is causing this.

Thank you Stackoverflow community!

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discomurray On BEST ANSWER

Are these Submodules possibly?

$ git submodule init
$ git submodule update

After a checkout should populate those empty directories.