Enable war deployment model (#197)

* Add 'home' files into build war artifact

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

* Disable copying exploded war to Tomcat dir

- hardcode vivo.all.log file name
- must now set system property: -Dvivo-dir=/opt/vivo/home/

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

* Ensure build does not remove and re-add VIVO_HOME/rdf

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

* Remove unnecessary profile from installer/pom.xml

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

* Rename example config files to have 'default' prefix

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: app name (#2)

* Non-functional change to comment in example.applicationSetup.n3

Related to: https://jira.lyrasis.org/browse/VIVO-1741

* Update orcidConfirm.ftl (#199)

* remove example-settings.xml
* simplify war name and afford override during build
* default app name to vivo and pass into context.xml

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: L.O <53535673+lb-ov@users.noreply.github.com>

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: William Welling <wwelling@library.tamu.edu>
Co-authored-by: L.O <53535673+lb-ov@users.noreply.github.com>

installer/webapp/src/main/webResources/META-INF/context.xml

@@ -1,9 +1,52 @@
 <Context> <!-- useHttpOnly="false" -->
+
+   <!--
+     # The 'home' property specifies the location of VIVO HOME.
+     # The system user used to run the VIVO web application must have write access
+     # to the parent directory of the directory defined in this property, if VIVO HOME
+     # does not already exist.
+     # If this directory already exists, the system user used to run the VIVO web application
+     # must have write access to this directory.
+   -->
    <Environment
         type="java.lang.String" 
         name="vitro/home"
         value="${vivo-dir}" override="true"/>
 
+   <!--
+     # The name of the application (possibly not used).
+   -->
+   <Environment
+           type="java.lang.String"
+           name="vitro/appName"
+           value="${app-name}" override="true"/>
+
+   <!--
+     # 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.
+   -->
+   <Environment
+           type="java.lang.String"
+           name="vitro/rootUserAddress"
+           value="vivo_root@mydomain.edu" override="true"/>
+
+   <!--
+     # 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/
+   -->
+   <Environment
+           type="java.lang.String"
+           name="vitro/defaultNamespace"
+           value="http://vivo.mydomain.edu/individual/" override="true"/>
+
    <!-- Disable persist sessions on shut down.-->
    <Manager pathname="" />
 </Context>

installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties

@@ -24,7 +24,7 @@
 # debug.log4j.properties exists will be used instead, if it exists, but is not stored in Subversion.
 
 log4j.appender.AllAppender=org.apache.log4j.RollingFileAppender
-log4j.appender.AllAppender.File= ${catalina.base}/logs/${app-name}.all.log
+log4j.appender.AllAppender.File= ${catalina.base}/logs/vivo.all.log
 log4j.appender.AllAppender.MaxFileSize=10MB
 log4j.appender.AllAppender.MaxBackupIndex=10
 log4j.appender.AllAppender.layout=org.apache.log4j.PatternLayout