Update Atlas and PME

[rnc]

Requires project-ncl/pom-manipulation-ext#1076 merged first.

General comments:

• Atlas changed its package structure (from org.commonjava.maven.atlas.ident.ref to org.commonjava.atlas.maven.ident.ref
• We have to exclude logback as other dependent components use the 1.5.x line but that is JDK11. We override back to the 1.3.x line.
• PME's FileIO no longer relies upon Galley (as that is JDK11).
  • Also exclude Galley from inclusion as GME doesn't use it and its JDK11
• PME has migrated groupId (from org.commonjava.maven.ext to org.jboss.pnc.maven-manipulator)
• Updated Sonatype snapshot URL
• Shadow jar configuration:
  • Removed relocation as that isn't required now with Downgrade OpenTelemetry. Fix dependency conflicts opentelemetry-ext-cli-java#17 and the fix for incorrect okhttp/okio dependencies bringing in the wrong versions of kotlin.
  • Ensured logback isn't removed from the CLI jar during minimisation (as its now excluded from e.g. PME dependencies).

[codecov]

Codecov Report

❌ Patch coverage is 84.61538% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.72%. Comparing base (c90170e) to head (bb687ab).
⚠️ Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
...in/java/org/jboss/gm/common/utils/GroovyUtils.java	71.42%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #516      +/-   ##
==========================================
+ Coverage   80.26%   80.72%   +0.45%     
==========================================
  Files          42       42              
  Lines        2600     2599       -1     
  Branches      356      357       +1     
==========================================
+ Hits         2087     2098      +11     
+ Misses        383      374       -9     
+ Partials      130      127       -3     

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