update documentation to reference Tomcat 7, Java 7 and newer apache config file name conventions. https://projects.ecoinformatics.org/ecoinfo/issues/6855
add notes about when metacat-index.war and metacatui.war files should be deployed.
add step about enabling CGI module.https://projects.ecoinformatics.org/ecoinfo/issues/6678
remove unnecessary Make step in registry installation instructions.https://projects.ecoinformatics.org/ecoinfo/issues/6678
Add the code to install the build-essential package.
merge updates from 2.4.2 changes
update documentation for trunk to use 2.5.0 release number
remove semantic annotation proposal - moved to github: https://github.com/DataONEorg/sem-prov-design/blob/master/docs/use-cases/semantics/semantic-annotation.md
add more sections about extending the annotation model, serializations, and permissions.
Added more description for the model. cleaned up a few formatting issues.
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