Resolve issue when merging TCIA-5_0 and TCIA-5_2 into TCIA-MASTER

Removed several 5.0 software source directories that inadvertently ended up at
the top level of the merged directory tree.  The directories had been moved to
the "software" subdirectory of the 5.2, and the merged missed that relocation.
Merge tag 'NBIA-MASTER-6_0-20140317-1' into TCIA-master

Fixed GUI and Rest API Performance issue

Conflicts:
	software/nbia-ctp/src/gov/nih/nci/nbia/dbadapter/NCIADatabase.java
	software/nbia-domain/.gitignore
	software/nbia-download/.gitignore
	software/nbia-web/src/ncia_messages.properties
	software/nbia-web/webapp/HTML/LoginFailure.html
	software/nbia-web/webapp/HTML/help/Application Support.10.1.html
	software/nbia-web/webapp/HTML/help/Getting Started.3.2.html
	software/nbia-web/webapp/HTML/help/Getting Started.3.5.html
	software/nbia-web/webapp/WEB-INF/facelets/bodyHome.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/layout/appFooter.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/layout/appHeader.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/layout/footer.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/layout/mainLayoutTemplate.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/layout/mainMenu.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/layout/quickLinks.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/layout/subMenu.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/welcome.xhtml
	software/nbia-web/webapp/WEB-INF/facelets/welcomeText.xhtml
	software/nbia-web/webapp/css/styleSheet.css
	software/nbia-web/webapp/sessionExpired.jsp
	software/ncia-core-grid-transfer/.gitignore
Fix minor problems found in review of merge of NBIA 6.1 into the TCIA master branch.
Fix minor merge issues from NBIA 6.0 found on review with a different comparison tool.
Merge branch 'TCIA-master' into TCIA-6_0
Modify install.properties to fit TCIA's base enviroment.

The file must still be edited to be useful by replacing the "CHANGE-ME" to correct values for the particular server being built.