Adding additional filters to pom.xml

Removes shade warnings from classes included in multiple dependencies
- Duplicate demo classes from biojava3-structure and biojava3-structure-gui
- vecmath and cli from jmol
- apache collections from beanutils
Fix CeSymmMainTest to reflect the sample input file

This should have been included in a9ee5b6e0ed512e667b7e29c62b1a23c1ab7d6b5
Major CeSymmMain improvements.

- Additional output formats implemented: PDB, HTML, TSV
- Improved documentation