diff --git a/.github/workflows/root-ci-config/build_root.py b/.github/workflows/root-ci-config/build_root.py
index 27e49bb7049fc..8be928158c137 100755
--- a/.github/workflows/root-ci-config/build_root.py
+++ b/.github/workflows/root-ci-config/build_root.py
@@ -143,7 +143,8 @@ def main():
             build_utils.print_warning(f'Failed to download: {err}')
             args.incremental = False
 
-    git_pull("src", args.repository, args.base_ref)
+    if not args.source_dir:
+        git_pull("src", args.repository, args.base_ref)
 
     benchmark: bool = 'rootbench' in options_dict and options_dict['rootbench'] == "ON"
     if benchmark:
@@ -166,7 +167,10 @@ def main():
         # Delete all the .gcda files produces by an artefact.
         build_utils.remove_file_match_ext(WORKDIR, "gcda")
 
-    build(options, args.buildtype)
+    if args.source_dir:
+        build(options, args.buildtype, source_dir=args.source_dir)
+    else:
+        build(options, args.buildtype)
 
     # Build artifacts should only be uploaded for full builds, and only for
     # "official" branches (master, v?-??-??-patches), i.e. not for pull_request
@@ -227,6 +231,7 @@ def parse_args():
     parser.add_argument("--pull_repository", default="",        help="Url to the pull request incoming repository")
     parser.add_argument("--head_ref",        default=None,      help="Ref to feature branch; it may contain a :<dst> part")
     parser.add_argument("--head_sha",        default=None,      help="Sha of commit that triggered the event")
+    parser.add_argument("--source_dir",       default=None,      help="Don't check out. Just use the source dir provided here.")
     parser.add_argument("--binaries",        default="false",   help="Whether to create binary artifacts")
     parser.add_argument("--architecture",    default=None,      help="Windows only, target arch")
     parser.add_argument("--repository",      default="https://github.com/root-project/root.git",
@@ -242,7 +247,7 @@ def parse_args():
     args.binaries = args.binaries.lower() in ('yes', 'true', '1', 'on')
     args.upload_artifacts = args.upload_artifacts.lower() in ('yes', 'true', '1', 'on')
 
-    if not args.base_ref:
+    if not args.base_ref and not args.source_dir:
         die(os.EX_USAGE, "base_ref not specified")
 
     if not args.platform_config: # If nothing special, we take the standard platform configuration, called as the platform
@@ -396,8 +401,11 @@ def archive_and_upload(archive_name, prefix):
 
 
 @github_log_group("Configure")
-def cmake_configure(options, buildtype):
-    srcdir = os.path.join(WORKDIR, "src")
+def cmake_configure(options, buildtype, **kwargs):
+    if 'source_dir' in kwargs:
+        srcdir = kwargs['source_dir']
+    else:
+        srcdir = os.path.join(WORKDIR, "src")
     builddir = os.path.join(WORKDIR, "build")
 
     # Add a private option to make the CI build faster by not changing the
@@ -445,16 +453,16 @@ def cmake_build(buildtype):
         die(result, "Failed to build")
 
 
-def build(options, buildtype):
+def build(options, buildtype, **kwargs):
     if not os.path.isdir(os.path.join(WORKDIR, "build")):
         builddir = os.path.join(WORKDIR, "build")
-        result = subprocess_with_log(f"mkdir {builddir}")
+        result = subprocess_with_log(f"mkdir -p {builddir}")
 
         if result != 0:
             die(result, "Failed to create build directory")
 
     if not os.path.exists(os.path.join(WORKDIR, "build", "CMakeCache.txt")):
-        cmake_configure(options, buildtype)
+        cmake_configure(options, buildtype, **kwargs)
     else:
         cmake_dump_config()
 
diff --git a/.github/workflows/root-docs-ci.yml b/.github/workflows/root-docs-ci.yml
index 1cd64060689c3..76dc6b10f5112 100644
--- a/.github/workflows/root-docs-ci.yml
+++ b/.github/workflows/root-docs-ci.yml
@@ -1,27 +1,35 @@
 name: 'ROOT Docs CI'
 
 on:
+  pull_request:
+    paths:
+      - '.github/workflows/root-docs-ci.yml'
+      - 'documentation/doxygen/**'
+    branches:
+      - 'master'
 
-  # Allows nightly builds to trigger one run for each branch easily, by
-  # providing the relevant branch as "default" value here:
   workflow_call:
-    inputs:
-      incremental:
-        type: boolean
-        default: true
 
   workflow_dispatch:
     inputs:
-      incremental:
-        description: 'Do full build'
-        type: boolean
+      eos_upload_directory:
+        description: 'Make documentation available at <root-website>/doc/<directory>. Leave empty for skipping the upload to eos.'
+        type: string
         required: false
-        default: false
-      # docu_input: # opportunity: overwrite makeinput.sh with these args
-      #   description: Folders to build documentation for. All folders are built if empty.
-      #   type: string
-      #   default: ""
-      #   required: false
+        default: 'master'
+
+env:
+  PLATFORM: alma10
+  DOC_DIR: ${{ case(github.base_ref == null, github.ref_name, 'PullRequest') }}
+  DOC_LOCATION: /github/home
+  EOS_DIR_NAME: |-
+    ${{ case(
+      inputs.eos_upload_directory != null, inputs.eos_upload_directory,
+      github.base_ref != null, 'PR',
+      github.ref_name
+      )
+    }}
+  TAR_FILE: html${{ case(github.base_ref == null, github.ref_name, '_PullRequest') }}.tar.gz
 
 jobs:
   build-docs:
@@ -32,20 +40,14 @@ jobs:
       - linux
       - x64
 
-    env:
-      PLATFORM: alma9
-      DOC_DIR: master
-      DOC_LOCATION: /github/home
-      BASE_REF: master
-      WEB_DIR_NAME: master
-      TAR_NAME: htmlmaster.tar
-
     permissions:
       contents: read
 
     container:
-      image: registry.cern.ch/root-ci/alma9:buildready
+      image: registry.cern.ch/root-ci/alma10:buildready
       options: '--security-opt label=disable --rm'
+      volumes:
+        - alma10_ccache_volume:/github/home/.cache/ccache
       env:
         OS_APPLICATION_CREDENTIAL_ID: '7f5b64a265244623a3a933308569bdba'
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
@@ -57,96 +59,49 @@ jobs:
         PYTHONUNBUFFERED: true
 
     steps:
+    - name: Prepare qhelpgenerator
+      # Qt6's libexec executables are not in the PATH by default
+      run: |
+        QHELPGENERATOR=$(which qhelpgenerator) && echo "QHELPGENERATOR=${QHELPGENERATOR}" >> "${GITHUB_ENV}"
+        PATH=/usr/lib64/qt6/libexec/:${PATH} QHELPGENERATOR=$(which qhelpgenerator) && echo "QHELPGENERATOR=${QHELPGENERATOR}" >> "${GITHUB_ENV}"
+
     - name: Checkout
       uses: actions/checkout@v6
       with:
-        ref: ${{ env.BASE_REF }}
         fetch-depth: 0
 
     - name: Set up Python Virtual Env
       # if the `if` expr is false, `if` still has exit code 0.
       # if the `if` block is entered, the block's exit code becomes the exit
       # code of the `if`.
-      run: 'if [ -d /py-venv/ROOT-CI/bin/ ]; then . /py-venv/ROOT-CI/bin/activate && echo PATH=$PATH >> $GITHUB_ENV; fi'
-
-    - name: Set up directory name and tar filenames
-      run: |
-        echo TAR_NAME=html${BASE_REF}.tar >> $GITHUB_ENV
-        echo DOCDIR_NAME=${BASE_REF} >> $GITHUB_ENV
-
-    # TODO: install latest versions in image on root-ci-images
-    - name: Install Doxygen 1.10.0
-      run : |
-        mkdir -p ${{ github.workspace }}/doxygen
-        curl -L https://github.com/doxygen/doxygen/releases/download/Release_1_10_0/doxygen-1.10.0.linux.bin.tar.gz | tar -xz -C ${{ github.workspace }}/doxygen/ --strip-components=1
-        echo PATH=$PATH:${{ github.workspace }}/doxygen/bin >> $GITHUB_ENV
-#         git clone --branch Release_1_12_0 https://github.com/doxygen/doxygen.git
-#         cd doxygen
-#         mkdir build
-#         cd build
-#         cmake ..
-#         make -j$(nproc)
-#         echo PATH=$PATH:${{ github.workspace }}/doxygen/build/bin >> $GITHUB_ENV
-#         cd ${{ github.workspace }}
-#         doxygen --version
-
-    - name: Install qhelpgenerator-qt5
-      run: |
-        dnf upgrade -y
-        dnf install -y qt5-doctools
-        which qhelpgenerator-qt5
+      run: 'if [ -d /py-venv/ROOT-CI/bin/ ]; then . /py-venv/ROOT-CI/bin/activate && echo ${PATH%:*} >> "${GITHUB_PATH}"; fi'
 
-    - name: Apply option overrides
-      env:
-        OVERRIDES: "testing=Off roottest=Off"
-        CONFIGFILE: '.github/workflows/root-ci-config/buildconfig/alma9.txt'
-      shell: bash
-      run: |
-        set -x
-        echo '' >> "$CONFIGFILE"
-        for ENTRY in $OVERRIDES; do
-            KEY=$( echo "$ENTRY" | cut -d '=' -f 1 )
-            # Add entry to file if not exists, otherwise replace
-            if grep -q "$KEY=" "$CONFIGFILE"; then
-                sed -i "s/$KEY=.*\$/$ENTRY/" "$CONFIGFILE"
-            else
-                echo "$ENTRY" >> "$CONFIGFILE"
-            fi
-        done
-        cat "$CONFIGFILE" || true
-
-    - name: Build ROOT - Workflow Dispatch
-      if:   github.event_name == 'workflow_dispatch'
-      env:
-          INCREMENTAL: ${{ inputs.incremental == 'true' }}
+    - name: Build ROOT
       run: ".github/workflows/root-ci-config/build_root.py
                   --buildtype      Release
                   --platform       ${{ env.PLATFORM }}
-                  --incremental    ${{ env.INCREMENTAL }}
-                  --base_ref       ${BASE_REF}
-                  --head_ref       ${BASE_REF}
-                  --binaries       false
-                  --repository     ${{ github.server_url }}/${{ github.repository }}"
-
-    - name: Build ROOT - Schedule
-      if:   github.event_name == 'schedule'
-      run: ".github/workflows/root-ci-config/build_root.py
-                  --buildtype      Release
-                  --platform       ${{ env.PLATFORM }}
-                  --incremental    ${{ inputs.incremental }}
-                  --base_ref       ${BASE_REF}
-                  --head_ref       ${BASE_REF}
-                  --binaries       false
-                  --repository     ${{ github.server_url }}/${{ github.repository }}"
+                  --incremental    false
+                  --source_dir     ${GITHUB_WORKSPACE}
+                  --repository     ${{ github.server_url }}/${{ github.repository }}
+                  --overrides      testing=Off roottest=Off
+                  --upload_artifacts false
+                  --binaries         false"
 
     - name: Run Doxygen
-      working-directory: ${{ env.DOC_LOCATION }}
       shell: bash
       run: |
-        source ROOT-CI/build/bin/thisroot.sh
-        export DOXYGEN_OUTPUT_DIRECTORY=/github/home/${DOC_DIR}
-        cd ROOT-CI/src/documentation/doxygen
-        make -j `nproc --all`
+        source ${HOME}/ROOT-CI/build/bin/thisroot.sh
+        export DOXYGEN_OUTPUT_DIRECTORY="/github/home/${DOC_DIR}"
+        cd documentation/doxygen
+        make -j "$(nproc --all)"
+
+    - name: Clean temporary files
+      # These files are used when doxygen runs incrementally
+      shell: bash
+      run: |
+        cd "/github/home/${DOC_DIR}"
+        rm html/*.md5
+        rm html/*.map
 
     - name: Create documentation archives
       working-directory: ${{ env.DOC_LOCATION }}
@@ -154,27 +109,19 @@ jobs:
       run: |
         pwd
         ls -l
-        echo ${DOC_DIR}
-        echo ${TAR_NAME}
         ls -l ${DOC_DIR}
-        tar cf ${TAR_NAME} ${DOC_DIR}
-        gzip ${TAR_NAME}
+        tar -caf ${TAR_FILE} ${DOC_DIR}
         ls -l
 
-    #Upload to GitHub as an artifact
-    - name: Upload tar file for GH
+    - name: Upload tar file to github
       if:   ${{ !cancelled() }}
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
-        name: ${{env.TAR_NAME}}.gz
-        path: ${{env.DOC_LOCATION}}/${{env.TAR_NAME}}.gz
+        name: ${{env.TAR_FILE}}
+        path: ${{env.DOC_LOCATION}}/${{env.TAR_FILE}}
         if-no-files-found: error
-
-    - name: Install Kerberos utilities
-      run: dnf -y install krb5-workstation
-
-    - name: Install XRootD client
-      run: dnf -y install xrootd-client
+        archive: false
+        retention-days: 8
 
     - name: Sync documentation to EOS
       env:
@@ -185,26 +132,29 @@ jobs:
         EOS_BASE_PATH: /eos/project/r/root-eos/website/
         EOS_ENDPOINT: root://eosproject-r.cern.ch
         KRB5CCNAME: /tmp/krb5cc
+      if: ${{ env.KRB5REALM != '' && env.EOS_DIR_NAME != null && env.EOS_DIR_NAME != '' }}
       working-directory: ${{ env.DOC_LOCATION }}
       # Because of https://github.com/xrootd/xrootd/issues/2235 , the xrd client can copy
       # only at most 65536 in one go. For this reason, we copy files in batches, dividing
       # them by extension. Once that is fixed in XRootD, a single command can be used
       # instead.
       run: |
+        echo "Input eos directory: ${EOS_DIR_NAME}"
+        EOS_DIR_NAME="${EOS_DIR_NAME%-00-patches}"
+        EOS_DIR_NAME="${EOS_DIR_NAME/-/}"
+        echo "Uploading to the directory: ${EOS_DIR_NAME}"
         failure=0
-        echo ${RWEBEOS_KT} | base64 -d > ${KT_FILE_NAME}
-        kinit -p ${{ secrets.KRB5USER }}@${{ secrets.KRB5REALM }} -kt ${KT_FILE_NAME}
-        cd ${DOC_DIR}/html/
-        rm -rf *.map # Intermediate files to create dot graphs
-        rm -rf *.md5 # As above
-        xrdcp --parallel 64 -rf ./*.html ${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${WEB_DIR_NAME} || failure=1
-        rm -rf *.html
-        xrdcp --parallel 64 -rf ./*.svg ${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${WEB_DIR_NAME} || failure=1
-        rm -rf *.svg
-        xrdcp --parallel 64 -rf ./ ${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${WEB_DIR_NAME} || failure=1
+        echo "${RWEBEOS_KT}" | base64 -d > "${KT_FILE_NAME}"
+        kinit -p ${{ secrets.KRB5USER }}@${{ secrets.KRB5REALM }} -kt "${KT_FILE_NAME}"
+        cd "${DOC_DIR}/html/"
+        xrdcp --parallel 64 -rf ./*.html "${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${EOS_DIR_NAME}" || failure=1
+        rm -rf ./*.html
+        xrdcp --parallel 64 -rf ./*.svg "${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${EOS_DIR_NAME}" || failure=1
+        rm -rf ./*.svg
+        xrdcp --parallel 64 -rf ./ "${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${EOS_DIR_NAME}" || failure=1
         cd ..
         rm -r html
-        xrdcp --parallel 64 -rf ./ ${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${WEB_DIR_NAME} || failure=1
+        xrdcp --parallel 64 -rf ./ "${EOS_ENDPOINT}/${EOS_BASE_PATH}/doc/${EOS_DIR_NAME}" || failure=1
         cd ..
-        xrdcp -rf ${TAR_NAME}.gz ${EOS_ENDPOINT}/${EOS_BASE_PATH}/download || failure=1
-        exit $failure
+        xrdcp -rf "${TAR_FILE}" "${EOS_ENDPOINT}/${EOS_BASE_PATH}/download" || failure=1
+        exit "$failure"
diff --git a/documentation/doxygen/Doxyfile b/documentation/doxygen/Doxyfile
index a46142f3c676f..79433c26ee0ec 100644
--- a/documentation/doxygen/Doxyfile
+++ b/documentation/doxygen/Doxyfile
@@ -1699,7 +1699,7 @@ QHP_SECT_FILTER_ATTRS  =
 # run qhelpgenerator on the generated .qhp file.
 # This tag requires that the tag GENERATE_QHP is set to YES.
 
-QHG_LOCATION           = qhelpgenerator-qt5
+QHG_LOCATION           = $(QHELPGENERATOR)
 
 # If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
 # generated, together with the HTML files, they form an Eclipse help plugin. To
diff --git a/documentation/doxygen/Makefile b/documentation/doxygen/Makefile
index 7b22aadb1a11a..1b1a9b5d008a7 100644
--- a/documentation/doxygen/Makefile
+++ b/documentation/doxygen/Makefile
@@ -77,6 +77,9 @@ doxygen: filter pyzdoc htmlfooter
 	$(call MkDir,$(DOXYGEN_EXAMPLE_PATH))
 	$(call MkDir,$(DOXYGEN_NOTEBOOK_PATH))
 	./makeinput.sh
+	echo "*** Diff of config file with default template:"
+	doxygen -x
+	echo "*** Run doxygen"
 	doxygen
 	bash ./CleanNamespaces.sh
 	gzip $(DOXYGEN_IMAGE_PATH)/ROOT.tag
diff --git a/documentation/doxygen/converttonotebook.py b/documentation/doxygen/converttonotebook.py
index bb13fb99d0625..f4cb4f6bc701d 100755
--- a/documentation/doxygen/converttonotebook.py
+++ b/documentation/doxygen/converttonotebook.py
@@ -423,7 +423,7 @@ def findBracedBlock(text, startpos, openingBraceChar):
 
 
 def findStuffBeforeFunc(text, searchStart, searchEnd):
-    beforeFunctionRe = re.compile("(;|}|//[^\n]*)\s*$", flags = re.MULTILINE)
+    beforeFunctionRe = re.compile("(;|}|//[^\n]*)\\s*$", flags = re.MULTILINE)
     try:
         # Find the last '}' or comment line etc before function definition:
         lastMatchBeforeFunc = [thisMatch for thisMatch in beforeFunctionRe.finditer(text, searchStart, searchEnd)][-1]
@@ -622,7 +622,7 @@ def changeString(matchObject):
         matchString = matchString.replace("THISISASPACE" , " ")
         return matchString
 
-    newcode = re.sub("#\s\s?\w\s[\w-]\s\w.*", changeString , code)
+    newcode = re.sub(r"#\s\s?\w\s[\w-]\s\w.*", changeString , code)
     return newcode
 
 def declareNamespace(code):