Publishing and Self-Archiving Recently I had a paper accepted by a major journal in discrete mathematics. Now the paper is going through the final stages of publication. The publisher sent me a link in which I have to specify the access policy for the paper. I can choose to either pay a fee (which I won't), and make my paper publicly available from the publisher website, or I can choose to self-archive, and 
then make my paper publicly available after a period of 24 months of embargo. 
More precisely, the text for the self-archiving is the following: 


  I wish to self-archive my accepted author manucript , which is my draft
      version of the article and which may include any author-incorporated 
      changes from the peer review process. I can post this author manuscript 
      on my institutional or subject-orientated repository immediately for
      internal use and make it publicly available after a journal specific
      embargo period has expired. 


The problem is that I have already posted the revised version of my paper at arxiv much before receiving this access form from the publisher. So I have some questions concerning this paragraph. 


The paragraph says that I can post the manuscript at a subject-oriented repository immediately for internal use. As mentioned before I already posted it to arxiv, which I think can be considered as a subject-oriented repository. Is that allowed? What do they mean by internal use?  
What do they mean about making the manuscript publicly available after the embargo? I have a link at my homepage pointing to the arxiv page. Is this considered to be publicly available? 
What is the difference between posting it to a repository and making it public? 
Can I get in trouble if they find the link to the paper at my homepage?
The text you quote is from Elsevier, and their policy on hosting articles says that "arXiv and RePEc can update a preprint immediately with the accepted manuscript and a DOI link to the formal publication" (while the embargo period applies only to other organizations), so you haven't violated the agreement in updating the arXiv posting.  You can add the DOI via the arXiv's journal reference feature once it is available.