This is how I would change the Jenkins job to work with the revised doctools configuration: https://review.typo3.org/#/c/41203/9/Configuration/Settings.yaml https://review.typo3.org/#/c/41204/1/Configuration/Settings.yaml

jenkins-flow-master.sh

# skipping everything above the next line
php composer.phar require --no-progress --no-interaction 'typo3/doctools:dev-master'

FLOW_CONTEXT=Production ./flow typo3.flow:cache:flush
FLOW_CONTEXT=Production ./flow typo3.flow:cache:warmup

FLOW_CONTEXT=Production ./flow typo3.doctools:commandreference:rendercollection Flow
FLOW_CONTEXT=Production ./flow typo3.doctools:reference:rendercollection Flow

# run this in Development - Production doesn't have the needed reflection data
./flow typo3.doctools:reference:rendercollection Flow:Signals

cd Packages/Framework/TYPO3.Flow
git add Documentation
git commit -m "[TASK] Update references in documentation" -m "See $BUILD_URL" -m "Releases: master" || true
git push origin master
cd -
# skipping clean up section

jenkins-flow-release.sh

# skipping everything above the next line
php composer.phar require --dev --no-progress --no-interaction typo3/doctools \*

./flow typo3.doctools:commandreference:rendercollection Flow
./flow typo3.doctools:reference:rendercollection Flow
./flow typo3.doctools:reference:rendercollection Flow:Signals

cd Packages/Framework/TYPO3.Flow
git add Documentation
git commit -m "[TASK] Update references in documentation" -m "See $BUILD_URL" -m "Releases: $BRANCH" || true
cd -
# skipping clean up section

jenkins-neos-master.sh

# skipping everything above the next line
php composer.phar require --no-progress --no-interaction 'typo3/doctools:dev-master'

FLOW_CONTEXT=Production ./flow typo3.flow:cache:flush
FLOW_CONTEXT=Production ./flow typo3.flow:cache:warmup

FLOW_CONTEXT=Production ./flow typo3.doctools:commandreference:rendercollection Neos
FLOW_CONTEXT=Production ./flow typo3.doctools:reference:rendercollection Neos

# run this in Development - Production doesn't have the needed reflection data
./flow typo3.doctools:reference:rendercollection Neos:Signals

cd Packages/Application/TYPO3.Neos

# When there is one + and one -, that's just changing the date in the file,
# So, don't pollute the git history with useless commits.
# Only commit changes for files with more than one changed files.
for unchanged in `git diff  --numstat | grep $'1\t1\t' | cut -f3`; do
	git checkout $unchanged;
done

git add Documentation
git commit -m "[TASK] Update references in documentation" -m "See $BUILD_URL" -m "Releases: master" || true
git push origin master
cd -

# skipping clean up section

jenkins-neos-release.sh

# skipping everything above the next line
php composer.phar require --no-progress --no-interaction typo3/doctools \*

./flow typo3.doctools:commandreference:rendercollection TYPO3.Neos
./flow typo3.doctools:reference:rendercollection Neos
./flow typo3.doctools:reference:rendercollection Neos:Signals

cd Packages/Application/TYPO3.Neos
#always commit, even if only dates have changed. That way "last updated" is the day of the last release.
git add Documentation
git commit -m "[TASK] Update references in documentation" -m "See $BUILD_URL" -m "Releases: $BRANCH" || true
cd -
# skipping clean up section

Especially note lines 18-20 which prevent committing any file that merely has an updated timestamp in it. Let's stop polluting our git history!

Used that in slightly adjusted form. Thanks for preparing this!