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>

home/src/main/resources/config/default.runtime.properties

@@ -9,19 +9,6 @@
 #
 # -----------------------------------------------------------------------------
 
-#
-# This namespace will be used when generating URIs for objects created in the
-# editor. In order to serve linked data, the default namespace must be composed
-# as follows (optional elements in parentheses):
-#
-# scheme + server_name (+ port) (+ servlet_context) + "/individual/"
-#
-# For example, Cornell's default namespace is:
-#
-# http://vivo.cornell.edu/individual/
-#
-Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/
-
 #
 # URL of Solr context used in local Vitro search. This will usually consist of:
 #     scheme + server_name + port + vitro_webapp_name + "solr"
@@ -70,13 +57,6 @@ VitroConnection.DataSource.dbtype = MySQL
 VitroConnection.DataSource.driver = com.mysql.jdbc.Driver
 VitroConnection.DataSource.validationQuery = SELECT 1
 
-#
-# The email address of the root user for the VIVO application. The password
-# for this user is initially set to "rootPassword", but you will be asked to
-# change the password the first time you log in.
-#
-rootUser.emailAddress = root@myDomain.com
-
 #
 # Argon2 password hashing parameters for time, memory and parallelism required to
 # compute a hash.