How to use widoco in terminal to generate documentation of the ontology:
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1) prepare the HTML files with sections (abstract, introduction, references, description)
2) fill in the metadata-config file (based on the Using a configuration section of https://github.com/dgarijo/Widoco/blob/master/doc/metadataGuide/guide.md), it is placed in ../agendovy/popis-dat/config-metadata for popis-dat ontology. Edit IRIs, version etc...
3) run widoco from JAR file with args, e.g.

/usr/lib/jvm/java-11-openjdk-amd64/bin/java -jar widoco-1.4.25-jar-with-dependencies_JDK-11.jar -confFile ../agendovy/popis-dat/config-metadata -htaccess -includeAnnotationProperties -ontFile ../agendovy/popis-dat/1.0.8/ontology.ttl -webVowl -uniteSections -outFolder ../agendovy/popis-dat/1.0.9/documentation

or 

/usr/lib/jvm/java-11-openjdk-amd64/bin/java -jar widoco-1.4.25-jar-with-dependencies_JDK-11.jar -confFile ../agendovy/popis-dat/config-metadata -htaccess -includeAnnotationProperties -ontURI https://raw.githubusercontent.com/kbss-cvut/popis-dat-ontology/main/model.ttl -webVowl -lang cs-en -rewriteAll -outFolder ../agendovy/popis-dat/1.0.9

where:
   -confFile PATH   ,references the metadata-config file
   -htaccess        ,generates .htaccess file
   -ontFile PATH    ,loads ontology file from the machine OR
   -ontURI PATH     ,loads ontoogy from URI
   -webVowl         ,creates visualization based on the WebVowl
   -uniteSections   ,writes all HTML into one file
   -outFolder PATH  ,specifies where to save generated documentation
   -lang LAN1-LAN2  ,specifies languages
   -rewriteAll      ,rewrites existing files

do not forget to rewrite paths to config-metadata, desired output and ontology URI or file.

4) copy sections into the new documentation folder, make sure the paths are correct.
5) check and eventually edit generated .htaccess file
6) add address to HTTPS enabled sites in apache
7) copy current versions of glosář, model and slovník from github as raw data using wget to the current version directory (1.0.9 in previous example)