Why won't changes to web.xml in deployment directory take effect in WebSphere?

Normally when a web application is deployed to WebSphere, the "exploded" .EAR file resides in a directory similar to

C:\Programs\IBM\WebSphere\AppServer\profiles\AppSrv01\installedApps\<your computer name here>Node01Cell\<EAR file name here>\<WAR file name here>

Most changes to files underneath this directory structure are reflected in the application after the web application is re-started.  However, making changes to web.xml here will not have any effect.  Instead, WebSphere stores a copy of web.xml in

C:\Programs\IBM\WebSphere\AppServer\profiles\AppSrv01\config\cells\<your computer name here>Node01Cell\applications\<EAR file name here>\deployments\<context root here>\<WAR file name here>\WEB-INF\web.xml

that it actually heeds.  Misleading, eh?

WebSphere, ADMA5006E, and java.lang.NullPointerException

After compiling some code with the Oracle JDK,

java version "1.8.0_20"
Java(TM) SE Runtime Environment (build 1.8.0_20-b26)
Java HotSpot(TM) 64-Bit Server VM (build 25.20-b23, mixed mode)

I deployed to WebSphere I got the following error:

ADMA5006E: An error occurred configuring [my application name] in WebSphere Application Server repository: java.lang.NullPointerException

After adjusting my JAVA_HOME to point at the WebSphere Java,

 java version "1.6.0"
Java(TM) SE Runtime Environment (build pwa6460_26sr7fp1ifix-20140220_01(SR7 FP1+
IX90136+IX90137))
IBM J9 VM (build 2.6, JRE 1.6.0 Windows 7 amd64-64 Compressed References 2013123
0_180580 (JIT enabled, AOT enabled)

I was able to deploy to WebSphere.  While the javac command did not specify the target Java version, and the version 1.8 byte code may have problems running on a version 1.6 platform, getting a java.lang.NullPointerException doesn't seem like well-written error handling?

Where do you find WebSphere Application Server port information?

For WAS 8.5.5.2, to find port information, on the left-side of the admin GUI, Servers > Server Types > WebSphere application servers.

Then, on the main part of the GUI, choose your server, then Configuration tab > Communication sub-section > Ports