Update files included with embedded distributions

[labkey-tchad]

Rationale

The service scripts and application.properties need some polish before we ship them.
server/configs/application.properties is used for dev deployments and TeamCity. This file should have a comprehensive list of available properties.
server/configs/webapps/embedded/config/application.properties is the one included in distributions. This should have a more pared down set of properties and won't have the @@value@@ placeholders used for string replacement by the gradle plugin.

Related Pull Requests

• Improve upgrade workflow for embedded Tomcat #752

Changes

• Tidy up application.properties files
• Remove some internal properties from properties included with distributions (CSP configs and json access log)
• Remove mentions of Tomcat from service scripts

[labkey-jony]

I tried this revised version in a recent test, but the variables do not appear to be respected.

For example, $LABKEY_HOME literally gets treated as the name of the folder, not as a substitution for /labkey/labkey. This causes a directory to be created called '$LABKEY_HOME' with the single-quotes with a path of /labkey/labkey/'$LABKEY_HOME'

In my original example file, I had to hardcode these paths for them to work as well.

https://gist.github.com/labkey-jony/12d8242e906947fa46a7b62f3238a522