Create vivo/home on application start-up (#192)

* Create vivo/home on application start-up

- Add logic for untarring vivo-home

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Require runtime.properties and applicationSetup.n3 be in 'config/' dir

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Support loading config files with or without 'default' prefix
* Prioritize without the prefix

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Add leading slash to location of vivo-home.tar resource path
* This allows for deployment in both Tomcat and Jetty

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Ensure VIVO_HOME is populated whether it is empty or not

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Require common properties to be in JNDI

Properties include:
- vitro/home
- vitro/appName
- vitro/rootUserAddress
- vitro/defaultNamespace

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* VIVO-1443: non destructive vivo home untarring (#2)

* Upgrade Jena version to 3.16.0 (#196)

Related to: https://jira.lyrasis.org/browse/VIVO-1943

* remove example-settings.xml
* update home directory untar non-destructive
* checksum digest to retain modified files
* compare checksum from digest with existing file
* overwrite files that have not changed
* add command to manually generate checksum digest
* simplify parsing checksum digest using pattern

Co-authored-by: Andrew Woods <awoods@lyrasis.org>
Co-authored-by: Andrew Woods <awoods@duraspace.org>

* not overwrite existing file if same as tar entry (#3)

* Upgrade Jena version to 3.16.0 (#196)

Related to: https://jira.lyrasis.org/browse/VIVO-1943

* remove example-settings.xml
* update home directory untar non-destructive
* checksum digest to retain modified files
* compare checksum from digest with existing file
* overwrite files that have not changed
* add command to manually generate checksum digest
* simplify parsing checksum digest using pattern
* do not overwrite file if same as already exists

Co-authored-by: Andrew Woods <awoods@lyrasis.org>
Co-authored-by: Andrew Woods <awoods@duraspace.org>

* Update log messages for clarity

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: William Welling <wwelling@library.tamu.edu>
Co-authored-by: Gross, Benjamin <benjamin.gross@clarivate.com>

api/src/test/java/edu/cornell/mannlib/vitro/webapp/controller/api/SparqlUpdateApiTest.java

@@ -73,7 +73,6 @@ public class SparqlUpdateApiTest extends AbstractTestClass {
         try {
             if(ds.supportsTransactions()) {
                 ds.begin(ReadWrite.WRITE);
-                System.out.println("yep");
             }
             UpdateAction.execute(UpdateFactory.create(updateStr1), graphStore);
         } finally {