What programs have trouble with case-sensitive (HFSX) filesystems, and how to fix them

There are some programs that require a case-sensitive filesystem, and others that require case-insensitive. Even though Apple warns against using case sensitive file systems, in some situations it is useful.

What programs have trouble with Case Sensitive (HFSX) systems?

What are the work-arounds?

In general, the problem is that the developers have a file in their app called FOO, but try to access the file by the name foo. In an HFS+ system that is case preserving but case insensitive, searching for foo will find FOO. That is not the case in HFSX. The general solution is therefore to

1. Find the misnamed file or folder
2. Make a copy, a link, or rename so the expected name is found