Migration improvement

[philips77]

This PR fixes a bug where Gradle Sync would fail if a library was in a sub-project, not under a root project, for example:

project
  \- libs
     \- dfu

Plugin 2.6 was adding dokka dependency to parent module, which in this case was :libs (and it didn't have Dokka set up).
This PR uses rootProject instead of parent.

Also, some warning messages were added to help with migration to Nordic Plugins 2.6+:

• Message to add org.jetbrains.dokka.experimental.gradle.pluginMode=V2Enabled in gradle.properties,
• Message to set up dokka for the root project.