Doxygen warnings in general are recognized. However the new warnings plugin cannot resolve the path and raises an error log message. Below the output:

[Doxygen] Searching for all files in '/srv/www/jenkins/workspace/st-Jenkins-WinTen-Extension-63MRU47OQSVYE4W4LDAQWFG2P6CRZMHRFO6K764RXP3I2QL3TGVQ' that match the pattern 'DoxygenOutput.txt'
[Doxygen] -> found 1 file
[Doxygen] Successfully parsed file /srv/www/jenkins/workspace/st-Jenkins-WinTen-Extension-63MRU47OQSVYE4W4LDAQWFG2P6CRZMHRFO6K764RXP3I2QL3TGVQ/DoxygenOutput.txt
[Doxygen] -> found 14 issues (skipped 1 duplicate)
[Doxygen] [ERROR] Can't resolve absolute paths for some files:
[Doxygen] [ERROR] - /pump/external/specific/arm/stm32f4xx/libinc/stm32f4xx_i2c.h
[Doxygen] [ERROR] - /pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_i2c.c
[Doxygen] [ERROR] - /pump/external/specific/arm/cmsis_dsp/MatrixFunctions/arm_mat_inverse_f32.c
[Doxygen] [ERROR] - /pump/external/specific/arm/cmsis/arm_math.h
[Doxygen] [ERROR] - /pump/external/specific/arm/cmsis_dsp/StatisticsFunctions/arm_min_q7.c
[Doxygen] [ERROR] - /pump/external/specific/arm/stm32f4xx/libinc/stm32f4xx_flash.h
[Doxygen] [ERROR] - /pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_gpio.c
[Doxygen] [ERROR] - /pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_flash.c
[Doxygen] [ERROR] Can't create fingerprints for some files:
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis/arm_math.h', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis/arm_math.h
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis/arm_math.h', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis/arm_math.h
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis/arm_math.h', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis/arm_math.h
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis/arm_math.h', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis/arm_math.h
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis/arm_math.h', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis/arm_math.h
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis_dsp/MatrixFunctions/arm_mat_inverse_f32.c', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis_dsp/MatrixFunctions/arm_mat_inverse_f32.c
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis_dsp/MatrixFunctions/arm_mat_inverse_f32.c', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis_dsp/MatrixFunctions/arm_mat_inverse_f32.c
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis_dsp/StatisticsFunctions/arm_min_q7.c', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis_dsp/StatisticsFunctions/arm_min_q7.c
[Doxygen] [ERROR] - '/pump/external/specific/arm/cmsis_dsp/StatisticsFunctions/arm_min_q7.c', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/cmsis_dsp/StatisticsFunctions/arm_min_q7.c
[Doxygen] [ERROR] - '/pump/external/specific/arm/stm32f4xx/libinc/stm32f4xx_flash.h', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/stm32f4xx/libinc/stm32f4xx_flash.h
[Doxygen] [ERROR] - '/pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_gpio.c', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_gpio.c
[Doxygen] [ERROR] - '/pump/external/specific/arm/stm32f4xx/libinc/stm32f4xx_i2c.h', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/stm32f4xx/libinc/stm32f4xx_i2c.h
[Doxygen] [ERROR] - '/pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_flash.c', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_flash.c
[Doxygen] [ERROR] - '/pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_i2c.c', IO exception has been thrown: java.nio.file.NoSuchFileException: /pump/external/specific/arm/stm32f4xx/libsrc/stm32f4xx_i2c.c
[Doxygen] Post processing issues on 'Master' with encoding 'UTF-8'
[Doxygen] Resolving absolute file names for all issues
[Doxygen] -> 0 resolved, 8 unresolved, 0 already resolved
[Doxygen] Copying affected files to Jenkins' build folder /srv/www/jenkins/jobs/code/branches/LIM-924-Test.9bmsp6.en-Extension/builds/90
[Doxygen] -> 0 copied, 0 not in workspace, 8 not-found, 0 with I/O error
[Doxygen] Resolving module names from module definitions (build.xml, pom.xml, or Manifest.mf files)
[Doxygen] -> resolved module names for 14 issues
[Doxygen] Resolving package names (or namespaces) by parsing the affected files
[Doxygen] -> resolved package names of 8 affected files
[Doxygen] No filter has been set, publishing all 14 issues
[Doxygen] Creating fingerprints for all affected code blocks to track issues over different builds
[Doxygen] -> created fingerprints for 0 issues
[Doxygen] Skipping blaming as requested in the job configuration

I think, I tracked down the problem to the preceeding slash in the path. However, when I trim it before passing the output file to this plugin, no warnings at all are found. Maybe this is a problem of the DoxygenParser in the analysis-model library.

Passing the full path to the plugin ends in the same path resolution problems as above, however, the warnings are found.