Added support for reading and writing app env variables into manifest
file. Modified IBM patch to also write the env variables.
PT 71498100: Fixed both regressions in manifest writing and jar
generation for Java standalone/Spring boot applications. 

PT 69578798: Modified publish operation such that they are no longer run
in a separate job, but in the same PublishJob launched by WST. This will
ensure that the browser will open once the publish operation is
completed in the PublishJob.
IBM Patch - PT 70118610 - Application start framework.
Merge pull request #7 from elsony/master

[71865404] Abstract implementation for AbstractAppStateTracker to monitor console output