On Linux, the operating system does not automatically search the current directory for shared libraries. The problem is likely that you need to set the load library path before trying to start the application. I just built the console app (it builds fine when the system is configured correctly), and when I try to run it without setting the path, here is what I see:
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$ ./GmatConsole
./GmatConsole: error while loading shared libraries: libGmatBase.so: cannot open shared object file: No such file or directory
However, if I type this line first, setting the load library path:
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$ export LD_LIBRARY_PATH=.
then the application loads correctly:
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$ ./GmatConsole
********************************************
*** GMAT Console Application
********************************************
General Mission Analysis Tool
Console Based Version
Build Date: May 13 2013 08:03:39
Moderator is creating core engine...
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