Generate features and dev mode, modifying pom.xml in multi module project errors

[kathrynkodama]

To reproduce
See the logic in MultiModuleUpdatePomsTests

With feature generation enabled, after war module's pom.xml is modified

ci.maven/liberty-maven-plugin/src/it/dev-it/src/test/java/net/wasdev/wlp/test/dev/it/MultiModuleUpdatePomsTest.java

Line 70 in a3d34f3

touchFileTwice("war/pom.xml");

generate features runs twice and on the second run throws an error:

[INFO] [INFO] guide-maven-multimodules-war source compilation was successful.
[INFO] [INFO] guide-maven-multimodules-war tests compilation was successful.
[INFO] [INFO] guide-maven-multimodules-ear tests compilation was successful.
[INFO] [INFO] Generating feature list from incremental changes...
[INFO] [INFO] Running liberty:generate-features
[INFO] [INFO] Parsing the server file /tmp/temp7486163829553659348/ear/src/main/liberty/config/server.xml for features and includes.
[INFO] [INFO] [AUDIT   ] CWWKT0017I: Web application removed (default_host): http://fv-az50-99.scfqo42wrlxuxg5qb0ygs2t2if.cx.internal.cloudapp.net:9080/converter/
[INFO] [INFO] [AUDIT   ] CWWKZ0009I: The application guide-maven-multimodules-ear has stopped successfully.
[INFO] [INFO] [AUDIT   ] CWWKT0016I: Web application available (default_host): http://fv-az50-99.scfqo42wrlxuxg5qb0ygs2t2if.cx.internal.cloudapp.net:9080/converter/
[INFO] [INFO] [AUDIT   ] CWWKZ0003I: The application guide-maven-multimodules-ear updated in 0.071 seconds.
[INFO] [INFO] Parsing the server file /tmp/temp7486163829553659348/ear/src/main/liberty/config/server.xml for features and includes.
[INFO] [INFO] No additional features were generated.
[INFO] [INFO] Running liberty:generate-features
[INFO] [INFO] Parsing the server file /tmp/temp7486163829553659348/ear/src/main/liberty/config/server.xml for features and includes.
Error: [ERROR] Failed to generate a working set of features. Error scanning the application for Liberty features: java.lang.NullPointerException.
[INFO] To disable the automatic generation of features, type 'g' and press Enter.

Expected Behaviour
Feature generation only runs once, no additional features are generated.

[kathrynkodama]

May be the same issue described: #1321 (comment)
but requires further investigation.

[kathrynkodama]

NPE should be fixed with OpenLiberty/ci.common#343 but still need to investigate why generate features is running twice