diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c269d5124c3a83a4115ad4c199fa1b96a3f9d5cc..051869fe4d94bc54b9d93d0a0eb9582048381d4c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,10 +46,10 @@ mkdocs:
   script:
   #- apt-get update
   #- apt-get -y install git
-  - bash add_version.sh
-  - bash get_modules.sh
+  - bash scripts/add_version.sh
+  - bash scripts/get_modules.sh
   - mkdocs build
-  - bash clean_json.sh site/mkdocs/search_index.json
+  - bash scripts/clean_json.sh site/mkdocs/search_index.json
   - sed -i 's,href="" title=",href="/" title=",g' site/404.html
   artifacts:
     paths:
diff --git a/docs.it4i/pbspro-documentation/pbspro.md b/docs.it4i/pbspro-documentation/pbspro.md
deleted file mode 100644
index 397d6e14ea8b7470fc15ee9a33bdda2b4effe62d..0000000000000000000000000000000000000000
--- a/docs.it4i/pbspro-documentation/pbspro.md
+++ /dev/null
@@ -1,4 +0,0 @@
-* ![pdf](../img/pdf.png)[PBSPro Programmer's Guide](src/pbspro-programmers-guide.pdf)
-* ![pdf](../img/pdf.png)[PBSPro Quick Start Guide](src/pbspro-quick-start-guide.pdf)
-* ![pdf](../img/pdf.png)[PBSPro Reference Guide](src/pbspro-reference-guide.pdf)
-* ![pdf](../img/pdf.png)[PBSPro User's Guide](src/pbspro-users-guide.pdf)
diff --git a/docs.it4i/pbspro-documentation/src/pbspro-programmers-guide.pdf b/docs.it4i/pbspro-documentation/src/pbspro-programmers-guide.pdf
deleted file mode 100644
index 0dedf4abdd8383d57404efbae0943baab3185d91..0000000000000000000000000000000000000000
Binary files a/docs.it4i/pbspro-documentation/src/pbspro-programmers-guide.pdf and /dev/null differ
diff --git a/docs.it4i/pbspro-documentation/src/pbspro-quick-start-guide.pdf b/docs.it4i/pbspro-documentation/src/pbspro-quick-start-guide.pdf
deleted file mode 100644
index 19748e9c286e4ab83e6d8ec872bb4d20958189ac..0000000000000000000000000000000000000000
Binary files a/docs.it4i/pbspro-documentation/src/pbspro-quick-start-guide.pdf and /dev/null differ
diff --git a/docs.it4i/pbspro-documentation/src/pbspro-reference-guide.pdf b/docs.it4i/pbspro-documentation/src/pbspro-reference-guide.pdf
deleted file mode 100644
index 10f4b7f116a69f53e188686b109172dba13ba6f1..0000000000000000000000000000000000000000
Binary files a/docs.it4i/pbspro-documentation/src/pbspro-reference-guide.pdf and /dev/null differ
diff --git a/docs.it4i/pbspro-documentation/src/pbspro-users-guide.pdf b/docs.it4i/pbspro-documentation/src/pbspro-users-guide.pdf
deleted file mode 100644
index 8c933ce03e23ee4df154ebec358c17f2b7becd2e..0000000000000000000000000000000000000000
Binary files a/docs.it4i/pbspro-documentation/src/pbspro-users-guide.pdf and /dev/null differ
diff --git a/docs.it4i/pbspro.md b/docs.it4i/pbspro.md
new file mode 100644
index 0000000000000000000000000000000000000000..72f5c3dd33b2946d0399ffe3c16c7cab8613a5b8
--- /dev/null
+++ b/docs.it4i/pbspro.md
@@ -0,0 +1,4 @@
+* ![pdf](img/pdf.png)[PBS Pro Programmer's Guide](http://www.pbsworks.com/pdfs/PBSProgramGuide13.0.pdf)
+* ![pdf](img/pdf.png)[PBS Pro Quick Start Guide](http://www.pbsworks.com/pdfs/PBSQuickStartGuide13.0.pdf)
+* ![pdf](img/pdf.png)[PBS Pro Reference Guide](http://www.pbsworks.com/pdfs/PBSReferenceGuide13.0.pdf)
+* ![pdf](img/pdf.png)[PBS Pro User's Guide](http://www.pbsworks.com/pdfs/PBSUserGuide13.0.pdf)
diff --git a/mkdocs.yml b/mkdocs.yml
index 7e21b8a0015a94225128237938c457b386d983a6..5a9bf6a77dc7b0ae2bb5d6d73299736677d7941d 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,6 +1,7 @@
 site_name: IT4Innovations Documentation
 theme_dir: 'material'
 docs_dir: docs.it4i
+site_favicon: img/favicon.ico
 
 extra_css: 
    - src/css.css
@@ -184,7 +185,7 @@ pages:
 #  - 'Software':
 #    - Modules Matrix: modules-matrix.md
   - Modules Matrix: modules-matrix.md
-  - PBS Pro Documentation: pbspro-documentation/pbspro.md
+  - PBS Pro Documentation: pbspro.md
 #  - Testing:
 #    - Colors: colors.md
 
diff --git a/add_version.sh b/scripts/add_version.sh
similarity index 100%
rename from add_version.sh
rename to scripts/add_version.sh
diff --git a/clean_json.sh b/scripts/clean_json.sh
similarity index 100%
rename from clean_json.sh
rename to scripts/clean_json.sh
diff --git a/cluster_modules.py b/scripts/cluster_modules.py
similarity index 100%
rename from cluster_modules.py
rename to scripts/cluster_modules.py
diff --git a/colors.sh b/scripts/colors.sh
similarity index 100%
rename from colors.sh
rename to scripts/colors.sh
diff --git a/get_cvs.sh b/scripts/get_cvs.sh
similarity index 100%
rename from get_cvs.sh
rename to scripts/get_cvs.sh
diff --git a/get_modules.sh b/scripts/get_modules.sh
similarity index 100%
rename from get_modules.sh
rename to scripts/get_modules.sh
diff --git a/scripts/modules.py b/scripts/modules.py
deleted file mode 100755
index a58c9747c3976e4ec40417495226c075800f5277..0000000000000000000000000000000000000000
--- a/scripts/modules.py
+++ /dev/null
@@ -1,95 +0,0 @@
-##!/usr/bin/env python
-#
-#  Copyright (C) 2016 IT4Innovations
-#
-##
-
-import json
-import os
-import re
-import xmlrpclib
-
-
-def software_list(class_path):
-    """List software from given module class"""
-    os.chdir(class_path)
-    software_list = next(os.walk('.'))[1]
-    # In case that there is 'all' module
-    if 'all' in software_list:
-        software_list.remove('all')
-    return software_list
-
-
-def get_software_versions(software_path):
-    """List available versions of software"""
-    os.chdir(software_path)
-    return next(os.walk('.'))[2]
-
-
-def get_module_description(module_path):
-    """Return software homepage URL and description"""
-    url = ""
-    description = " "
-    with open(module_path) as f:
-        content = f.read()
-    data = re.search(r"module-whatis\s{(Description: )?(.+)\s-\sHomepage:\s(\S+)}",
-                     content, re.DOTALL)
-    try:
-        description = data.group(2)
-        url = data.group(3)
-    except AttributeError:
-        pass
-    return url, description
-
-def push_to_portal(page):
-    """Push HTML page to the user portal"""
-    remote = 'https://admin_write_modules_table:IcifomHantyi@docs.it4i.cz/'
-    server = xmlrpclib.ServerProxy(remote)
-    xmlout = server.xmlrpc_salomon_list_of_modules(page)
-
-
-if __name__ == "__main__":
-    BASE_MODULES_DIR = '/apps/modules/'
-    SKIP_DIRS = ['all']
-    HTML_SOURCE_DATA = {}
-    os.chdir(BASE_MODULES_DIR)
-    subdirs = next(os.walk('.'))[1]
-    # Delete unwanted directories
-    for dir in SKIP_DIRS:
-        subdirs.remove(dir)
-
-    #print sorted(subdirs)
-    #subdirs = ['base']
-    # Create module class structure
-    print "# List of Available Modules"
-    for dir in sorted(subdirs):
-        class_path = os.path.join(BASE_MODULES_DIR, dir)
-        available_software = software_list(class_path)
-        #print available_software
-        print "\n###%s\n" % dir.title()
-        print "|Module|Description|Available versions|"
-        print "|--|--|--|"
-        HTML_SOURCE_DATA[dir] = {}
-        for soft in sorted(available_software, key=str.lower):
-            software_path = os.path.join(class_path, soft)
-            software_versions = get_software_versions(software_path)
-            # In case that there's not any available software version
-            if not software_versions:
-                continue
-            first_module_path = os.path.join(software_path, software_versions[0])
-            software_url, software_description = get_module_description(first_module_path)
-            #print software_description
-            HTML_SOURCE_DATA[dir][soft] = {'versions': [],
-                                           'url': software_url,
-                                           'description': software_description}
-            for version in software_versions:
-                HTML_SOURCE_DATA[dir][soft]['versions'].append(version)
-            #for version in software_versions:
-            #    HTML_SOURCE_DATA[dir][soft]['versions'].append(version)
-            if software_url=="":
-              print "|**%s**|%s|<nobr>%s</nobr>|" % (soft," ".join(software_description.split()),'</br>'.join(software_versions))
-            else:
-              print "|**[%s](%s)**|%s|<nobr>%s</nobr>|" % (soft,software_url," ".join(software_description.split()),'</br>'.join(software_versions))
-    #json_obj = json.dumps(HTML_SOURCE_DATA, sort_keys=True, indent=4)
-    #push_to_portal(json_obj)
-    #print json_obj
diff --git a/scripts/modules_compare.py b/scripts/modules_compare.py
deleted file mode 100755
index e45c06570f3f593c7df1eddbc928606f59ef381d..0000000000000000000000000000000000000000
--- a/scripts/modules_compare.py
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env python
-#
-#  Copyright (C) 2016 IT4Innovations
-#
-
-import os
-
-def software_list(class_path):
-    """List software from given module class"""
-    os.chdir(class_path)
-    software_list = next(os.walk('.'))[1]
-    # In case that there is 'all' module
-    if 'all' in software_list:
-        software_list.remove('all')
-    return software_list
-
-
-def get_software_versions(software_path):
-    """List available versions of software"""
-    os.chdir(software_path)
-    return next(os.walk('.'))[2]
-
-if __name__ == "__main__":
-    BASE_MODULES_DIR = '/apps/modules/'
-    SKIP_DIRS = ['all']
-    HTML_SOURCE_DATA = {}
-    os.chdir(BASE_MODULES_DIR)
-    subdirs = next(os.walk('.'))[1]
-    # Delete unwanted directories
-    for dir in SKIP_DIRS:
-        subdirs.remove(dir)
-
-    # Create module class structure
-    for dir in sorted(subdirs):
-        class_path = os.path.join(BASE_MODULES_DIR, dir)
-        available_software = software_list(class_path)
-        HTML_SOURCE_DATA[dir] = {}
-        for soft in sorted(available_software, key=str.lower):
-            software_path = os.path.join(class_path, soft)
-            software_versions = get_software_versions(software_path)
-            # In case that there's not any available software version
-            if not software_versions:
-                continue
-            first_module_path = os.path.join(software_path, software_versions[0])
-            HTML_SOURCE_DATA[dir][soft] = {'versions': []}
-            for version in software_versions:
-                HTML_SOURCE_DATA[dir][soft]['versions'].append(version)
-            print "%s|%s" % (soft.lower(),';'.join(software_versions))
diff --git a/scripts/motd.sh b/scripts/motd.sh
deleted file mode 100755
index 3d94de74b8f1278878b063ae094e869694c6fc0d..0000000000000000000000000000000000000000
--- a/scripts/motd.sh
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/bin/bash
-
-### MOTD and Downtime history
-# autor: kru0052
-# 2016 IT4Innovations
-# version 1.0
-###
-
-printf "update"
-wget -q  http://www.it4i.cz/support/?lang=en
-printf " ... OK\n"
-
-i="index.html?lang=en"
-
-HEAD=$(grep -n -m1 'class="matrix light-grey' "$i" |cut -f1 -d: | tr --delete '\n')
-END=$(grep -n -m1 '<h3>Other</h3>' "$i" |cut -f1 -d: | tr --delete '\n')
-LAST=$(wc -l "$i" | cut -f1 -d' ')
-DOWN=$((LAST-END+2))
-
-sed '1,'"$((HEAD-1))"'d' "$i" | sed -n -e :a -e '1,'"$DOWN"'!{P;N;D;};N;ba' | sed '/<div/d' > "TMP.html"
-rm "/srv/downtime/$i"
-
-title="Message of the day"
-head=$(cat TMP.html | grep "rss-item-title" | cut -d ">" -f 2 | cut -d "<" -f 1)
-date=$(cat TMP.html | grep "<i>" | cut -d ">" -f 2 | cut -d "<" -f 1 | cut -d " " -f 1)
-info=$(cat TMP.html | grep "<p>" | cut -d ">" -f 2 | cut -d "<" -f 1)
-rm /srv/downtime/TMP.html
-
-echo ""
-echo "$title"
-echo "$date - $head"
-echo "$info"
-echo ""
-
-# poovolene stavy - Salomon Maintenance, Anselm Maintenance, Back in Production, Infrastructure Maintenance, PBS Maintenance, SCRATCH Maintenance, HOME Maintenance, Salomon and Anselm Maintenance
-if [ "$head" = "Salomon Maintenance" ] || [ "$head" = "Anselm Maintenance" ] || [ "$head" = "Back in Production" ] || [ "$head" = "Infrastructure Maintenance" ] || [ "$head" = "PBS Maintenance" ] || [ "$head" = "SCRATCH Maintenance" ] || [ "$head" = "HOME Maintenance" ] || [ "$head" = "Salomon and Anselm Maintenance" ]; then
-	dateDown=$(cat /srv/downtime/docs/index.md | sed -n '/---/{n;p;}' | cut -d "|" -f 2 | cut -d " " -f 1)
-	headDown=$(cat /srv/downtime/docs/index.md | sed -n '/---/{n;p;}' | cut -d "|" -f 3 | cut -d "*" -f 3)	
-
-	echo "$date - $dateDown"
-
-
-	if [ "$date" = "$dateDown" ] && [ "$head" = "$headDown" ]; then
-		echo "Everything up-to-date..."
-	else
-		echo "Updating Downtime History..."
-		test=" |$date 00:00:00|**$head** $info|"
-		sed '/---/a '"$test"'' /srv/downtime/docs/index.md > /srv/downtime/TMP.md
-		cat /srv/downtime/TMP.md > /srv/downtime/docs/index.md
-	#	rm /srv/downtime/TMP.md
-	fi
-	
-#	echo "### $title" > docs/index.md
-#	echo "**$head**" >> docs/index.md
-#	echo "$date - $info" >> docs/index.md
-else
-	echo "Downtime History not updated..."
-fi
-
-       echo "# $title" > docs/motd.md
-       echo "**$head**" >> docs/motd.md
-       echo "$date - $info" >> docs/motd.md
-
-time=$(date)
-
-sed '$d' /srv/downtime/docs/index.md > /srv/downtime/TMP.md
-cat /srv/downtime/TMP.md > /srv/downtime/docs/index.md
-rm /srv/downtime/TMP.md
-echo "updating $time" >> /srv/downtime/docs/index.md 
diff --git a/scripts/html_md.sh b/scripts/preklopeni_dokumentace/html_md.sh
similarity index 100%
rename from scripts/html_md.sh
rename to scripts/preklopeni_dokumentace/html_md.sh
diff --git a/scripts/source/formatting b/scripts/preklopeni_dokumentace/source/formatting
similarity index 100%
rename from scripts/source/formatting
rename to scripts/preklopeni_dokumentace/source/formatting
diff --git a/scripts/source/lastFilter b/scripts/preklopeni_dokumentace/source/lastFilter
similarity index 100%
rename from scripts/source/lastFilter
rename to scripts/preklopeni_dokumentace/source/lastFilter
diff --git a/scripts/source/list_folder b/scripts/preklopeni_dokumentace/source/list_folder
similarity index 100%
rename from scripts/source/list_folder
rename to scripts/preklopeni_dokumentace/source/list_folder
diff --git a/scripts/source/list_image_mv b/scripts/preklopeni_dokumentace/source/list_image_mv
similarity index 100%
rename from scripts/source/list_image_mv
rename to scripts/preklopeni_dokumentace/source/list_image_mv
diff --git a/scripts/source/list_md_mv b/scripts/preklopeni_dokumentace/source/list_md_mv
similarity index 100%
rename from scripts/source/list_md_mv
rename to scripts/preklopeni_dokumentace/source/list_md_mv
diff --git a/scripts/source/list_rm b/scripts/preklopeni_dokumentace/source/list_rm
similarity index 100%
rename from scripts/source/list_rm
rename to scripts/preklopeni_dokumentace/source/list_rm
diff --git a/scripts/source/repairIMG b/scripts/preklopeni_dokumentace/source/repairIMG
similarity index 100%
rename from scripts/source/repairIMG
rename to scripts/preklopeni_dokumentace/source/repairIMG
diff --git a/scripts/source/replace b/scripts/preklopeni_dokumentace/source/replace
similarity index 100%
rename from scripts/source/replace
rename to scripts/preklopeni_dokumentace/source/replace
diff --git a/scripts/source/tab b/scripts/preklopeni_dokumentace/source/tab
similarity index 100%
rename from scripts/source/tab
rename to scripts/preklopeni_dokumentace/source/tab
diff --git a/scripts/source/tabREPLACE b/scripts/preklopeni_dokumentace/source/tabREPLACE
similarity index 100%
rename from scripts/source/tabREPLACE
rename to scripts/preklopeni_dokumentace/source/tabREPLACE