Adding exception handling for files with errors

Hello,

I ran javasphinx-apidoc against about 12000 java files in our codebase. The quality of the javadocs in these files is mixed and some are code-generated. I had a few crashes. When it crashed it stopped and you had to rerun it to find the next broken file.

This PR had some (very basic) error handling for these crashes so it prints out the problem file, the nature of the issue and continues processing. The file with the error will be missing from the output.

Perhaps someone who does more python can check I have used exceptions correctly.

Hope this helps,

Andrew