Handle `onConflict` setting for `include` elements related to application config

When gathering application names and locations from Liberty config files, they are added to a common collection with no regard to the onConflict setting for the <include> element that referenced the Liberty config file. The elements that are gathered from the Liberty config files are:

• XPATH_SERVER_APPLICATION = xPath.compile("/server/application");
• XPATH_SERVER_WEB_APPLICATION = xPath.compile("/server/webApplication");
• XPATH_SERVER_ENTERPRISE_APPLICATION = xPath.compile("/server/enterpriseApplication");

The methods that would need to query the onConflict setting and honor it are ServerConfigDocument.parseIncludeVariables and ServerConfigDocument.parseInclude. Also, the parseInclude method should probably call parseNames on the included file, just as it was called on the original config file in initializeAppsLocation. When merging multiple app elements for the same app, the id attribute is what connects them. Our code does not consider that attribute currently.

Start in ServerConfigDocument.parseIncludeVariables and parseInclude, then trace initializeAppsLocation and parseNames. Determine how each included application's id is merged and how the include element's onConflict setting should affect the three listed application XPath elements; done means included applications follow those rules consistently.