When my my Pipeline job calls the following:

        post {
                always {
                        junit "scripts/*.xml"
                        discoverReferenceBuild referenceJob: 'release-scripts/master'
                        recordCoverage(sourceDirectories: [[path: 'scripts']], tools: [[parser: 'COBERTURA', pattern: 'scripts/cover_db/cobertura.xml']])
{{                } }}
{{        } }}

with the attached file in scripts/cover_db/cobertura.xml, the coverage plugin produces the following output in the jenkins build log:
[Cobertura] Recording coverage results
[Cobertura] Searching for all files in '/var/lib/jenkins/workspace/release-scripts_master' that match the pattern 'scripts/cover_db/cobertura.xml'
[Cobertura] Traversing of symbolic links: disabled
[Cobertura] -> found 1 file
[Cobertura] Successfully parsed file '/var/lib/jenkins/workspace/release-scripts_master/scripts/cover_db/cobertura.xml'
[Cobertura] MODULE: 100.00% (1/1)
[Cobertura] PACKAGE: 100.00% (2/2)
[Cobertura] FILE: 100.00% (2/2)
[Cobertura] CLASS: 100.00% (2/2)
[Cobertura] LINE: 73.83% (79/107)
[Cobertura] LOC: 107
[Cobertura] Successfully processed file 'scripts/cover_db/cobertura.xml'
[Coverage] [-ERROR-] Errors while recording code coverage:
[Coverage] [-ERROR-] Errors during source path resolving:
[Coverage] [-ERROR-] Errors while resolving source files on agent:
[Coverage] [-ERROR-] Removing non-workspace source directory '/' - it has not been approved in Jenkins' global configuration.
[Coverage] [-ERROR-] - Skipping resolving of file: /usr/bin/prove (not part of workspace or permitted source code folders)
[Coverage] Recording coverage results
[Coverage] Searching for all files in '/var/lib/jenkins/workspace/release-scripts_master' that match the pattern 'scripts/cover_db/cobertura.xml'
[Coverage] Traversing of symbolic links: disabled
[Coverage] -> found 1 file
[Coverage] Successfully parsed file '/var/lib/jenkins/workspace/release-scripts_master/scripts/cover_db/cobertura.xml'
[Coverage] MODULE: 100.00% (1/1)
[Coverage] PACKAGE: 100.00% (2/2)
[Coverage] FILE: 100.00% (2/2)
[Coverage] CLASS: 100.00% (2/2)
[Coverage] LINE: 73.83% (79/107)
[Coverage] LOC: 107
[Coverage] Successfully processed file 'scripts/cover_db/cobertura.xml'
[Coverage] Resolving source code files...
[Coverage] Searching for source code files in:
[Coverage] -> /var/lib/jenkins/workspace/release-scripts_master/src/main/java
[Coverage] -> /var/lib/jenkins/workspace/release-scripts_master/scripts
[Coverage] -> finished resolving of absolute paths (found: 1, not found: 1)
[Coverage] Making paths of 1 source code files relative to workspace root...
[Coverage] Obtaining action of reference build
[Coverage] Obtaining reference build from reference recorder
[Coverage] -> Found 'release-scripts » master #44'
[Coverage] -> Using reference build 'release-scripts/master #44'
[Coverage] -> Found reference result in build '#44'
[Coverage] Calculating the code delta...
[Coverage] -> No delta calculator installed yet. You need to install the 'git-forensics' plugin to enable it for Git.
[Coverage] Calculating coverage deltas...
[Coverage] No quality gates have been set - skipping
[Coverage] Executing source code painting...
[Coverage] Painting 2 source files on agent
[Coverage] -> finished painting successfully
[Coverage] -> zipping sources from folder '/var/lib/jenkins/workspace/release-scripts_master/coverage' as '/var/lib/jenkins/workspace/release-scripts_master/coverage-sources.zip'
[Coverage] Copying painted sources from agent to build folder
[Coverage] -> extracting...
[Coverage] -> done
[Coverage] Deleting source code files of build #44
[Coverage] Finished coverage processing - adding the action to the build...
After this, it only reports coverage for "/usr/bin/prove" and "Zetes/DockerHandlers.pm", ignoring all other files.