Handle O/S windows covering IntelliJ

[turkeylurkey]

1. Sometimes an O/S window covers the Liberty tool window button. Need to click it and detect that it opened before continuing. If your click lands on the O/S window then the LTW will not open and an O/S window will open instead. So try clicking again to bring the IntelliJ window to the front and to open the LTW (openAndValidateLibertyToolWindow)
2. Wait for indexing right after opening the project window so it is done before other tests are run (waitForIndexing moved)
3. Added waitForIndexing to a few more tests
4. Indexing can take up to 1 minute before it starts
5. After adding xml wait a bit before checking the file (needed to fix one failing test in SingleModLibertyLSTestCommon)
6. Add logging to two methods for future debugging
7. The Stop button in the debugger can take up to 1 minute to appear in the UI

Fixes #913
Fixes #646

[aparnamichael]

Looks good!!

[aparnamichael]

@turkeylurkey There is some conflicts in the build.yaml file. Pleas take a look.

[TrevCraw]

Hi @turkeylurkey , the changes here look good, but I am wondering if you think they will still be necessary once we make the changes discussed earlier this week to enable our Liberty Tool Window to only display projects when IntelliJ has completed indexing (i.e. implement #985 for the Liberty Tool Window).