During the parse-hrefs-pass step of the XProc process a
.dita
file is not found message.
ERROR: resource not found: alfresco:/Sites/xxxx/documentLibrary/Sources/main/topics/new_topics/my_file.dita
There is an option called source-base-uri in the pipeline configuration file that defines the root of the folder structure for the source files. All of the files referenced either directly or indirectly from the source ditamap (or topic) need to be under that folder. That includes xref references, unless you specify the scope attribute to "external".
For example, if source-base-uri option is set as follows:
source-base-uri = alfresco:/Sites/xxxx/documentLibrary/Sources/main/ditamaps/
You probably need to move that one level up to
alfresco:/Sites/xxxx/documentLibrary/Sources/main/
documentLibrary
directory.