Steps to reproduce:
1. Create a symlink from a folder inside your $HOME, i.e. $HOME/symlink that goes to /home/someOtherLocation/
2. Create a new solution and project in $HOME/symlink/ , i.e. $HOME/symlink/testsol/testproj.csproj
3. Open solution that was just created, browsing it through $HOME.
4. Put a breakpoint in Program.cs, start debugging.
When the debugger stops, it opens a new file in MonoDevelop (/home/someOtherLocation/testsol/Program.cs).
Breakpoint should be hit in the currently opened Program.cs.
Pull request coming.
PR merged: https://github.com/mono/monodevelop/commit/32e25eaa9298cc97d324636f983561c3c2b223c3
Fixed in version 126.96.36.1994 (new-project-model)