diff --git a/.gitignore b/.gitignore
index a5ab7d5f5..d70fa0163 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,4 +14,5 @@ osal_lcov/
 outputOnFailure.txt
 cfe_ut_results.txt
 cfe_lcov_summary.txt
-cfe_lcov
\ No newline at end of file
+cfe_lcov
+*doc_logs/
\ No newline at end of file
diff --git a/runCFSscript.sh b/runCFSscript.sh
index 37a970c0c..082c62fa4 100755
--- a/runCFSscript.sh
+++ b/runCFSscript.sh
@@ -22,7 +22,7 @@ cat << EOF
     3) lcov.sh
     4) format-check.sh
     5) run-clang-format.sh
-    6) gen_cfe_usersguide.sh
+    6) dox.sh
     7) cfe_functionaltests.sh
     8) cfe_lcov.sh
 EOF
@@ -60,7 +60,7 @@ case $userNum in
         ./scripts/run-clang-format.sh "${userApp##*/}"
         ;;
     6)
-        ./scripts/gen_cfe_usersguide.sh
+        ./scripts/dox.sh "${userApp##*/}"
         ;;
     7)
         ./scripts/cfe_functionaltests.sh
diff --git a/scripts/dox.sh b/scripts/dox.sh
new file mode 100755
index 000000000..82e4559c6
--- /dev/null
+++ b/scripts/dox.sh
@@ -0,0 +1,104 @@
+#!/bin/bash
+
+applist="cf cs ds fm hk hs lc md mm sc"
+app=$1
+
+# generate documents with logs
+if [[ " $applist " =~ " $app " ]]; then
+    # build app usersguide (cFS application layer)
+    target="${app}-usersguide"
+
+    # clean
+    rm -rf ${app}_doc_logs
+    rm -rf sample_defs
+    rm -rf Makefile
+
+    # copy Files
+    cp ./cfe/cmake/Makefile.sample Makefile
+    cp -r ./cfe/cmake/sample_defs sample_defs
+
+    # add repo to build
+    app_list_line=$(cat sample_defs/targets.cmake | grep -o "list(APPEND MISSION_GLOBAL_APPLIST.*")
+    for i in "${app[@]}"
+    do
+        if [[ ${app_list_line} != *"$i"* ]];then
+            prev_app="sample_lib"
+            sed -i "s/$prev_app/& $i/" "sample_defs/targets.cmake";
+            prev_app=$i
+        fi
+    done
+
+    # setup build
+    make distclean
+    make prep
+
+    # dir
+    mkdir ${app}_doc_logs
+
+    # build document with logs
+    make -C build ${target} 2>&1 > ${app}_doc_logs/${target}_stdout.txt | tee ${app}_doc_logs/${target}_stderr.txt
+    mv build/docs/${target}/${target}-warnings.log ${app}_doc_logs/
+
+    # generate pdf
+    make -C ./build/docs/${target}/latex
+    mv build/docs/${target}/latex/refman.pdf ${app}_doc_logs/${target}.pdf
+
+elif [ ${app} = "osal" ]; then
+    # build osalapiguide
+    target="osal-apiguide"
+
+    osal_doc_logs="../osal_doc_logs"
+
+    cd osal
+
+    # clean
+    rm -rf ${osal_doc_logs}
+    rm -rf Makefile
+
+    # set up for build
+    cp Makefile.sample Makefile
+    make distclean
+    make prep
+
+    # dir
+    mkdir ${osal_doc_logs}
+
+    # build osal API guide
+    make ${target} 2>&1 > ${osal_doc_logs}/make_${target}_stdout.txt | tee ${osal_doc_logs}/make_${target}_stderr.txt
+    mv build/docs/${target}-warnings.log ${osal_doc_logs}/${target}-warnings.log
+
+elif [ ${app} = "cfe" ]; then
+    # List of targets
+    targets=("mission-doc" "cfe-usersguide")
+
+    cfe_doc_logs="cfe_doc_logs"
+
+    # clean
+    rm -rf ${cfe_doc_logs}
+    rm -rf sample_defs
+    rm -rf Makefile
+
+    # copy Files
+    cp ./cfe/cmake/Makefile.sample Makefile
+    cp -r ./cfe/cmake/sample_defs sample_defs
+
+    # set up for build
+    make distclean
+    make prep
+
+    # dir
+    mkdir ${cfe_doc_logs}
+
+    # Loop through the list of targets
+    for target in "${targets[@]}"; do
+        # build document with logs
+        make -C build ${target} 2>&1 > ${cfe_doc_logs}/${target}_stdout.txt | tee ${cfe_doc_logs}/${target}_stderr.txt
+        mv build/docs/${target}/${target}-warnings.log ${cfe_doc_logs}/
+        
+        # generate pdf
+        make -C ./build/docs/${target}/latex
+        mv build/docs/${target}/latex/refman.pdf ${cfe_doc_logs}/${target}.pdf
+    done
+else
+    echo -e "\nThe app provided doesn't match any available options. Try again!\n"
+fi
\ No newline at end of file
diff --git a/scripts/gen_cfe-usersguide.sh b/scripts/gen_cfe-usersguide.sh
deleted file mode 100644
index 2d4086837..000000000
--- a/scripts/gen_cfe-usersguide.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-
-# start fresh
-make distclean
-rm -rf sample_defs
-
-# declare document
-app=cfe-usersguide
-
-# copy Files
-cp ./cfe/cmake/Makefile.sample Makefile
-cp -r ./cfe/cmake/sample_defs sample_defs
-
-make prep
-
-# build document
-#make -C build $app 2>&1 > ${app}_stdout.txt | tee ${app}_stderr.txt
-make -C build cfe-usersguide 2>&1 > cfe-usersguide_stdout.txt | tee cfe-usersguide_stderr.txt
-mv build/docs/cfe-usersguide/cfe-usersguide-warnings.log .
-
-# generate pdf
-make -C ./build/docs/cfe-usersguide/latex
-mkdir deploy
-mv ./build/docs/cfe-usersguide/latex/refman.pdf ./deploy/cfe-usersguide.pdf
\ No newline at end of file
diff --git a/scripts/lcov.sh b/scripts/lcov.sh
index c4dc8d4d7..8d24fc774 100755
--- a/scripts/lcov.sh
+++ b/scripts/lcov.sh
@@ -1,3 +1,5 @@
+#!/bin/bash
+
 #apps
 #assumes these are all in the cFS/apps directory
 #and that they're all in lowercase