The LabKey Server documentation for client APIs is located here:
Hopefully, an API exists for the programming language of your choice. If not, you could use the "HTTP interface" and write a wrapper around it.
To query the data you need to be somewhat familiar with the database schema. If you are the administrator of your own LabKey Server installation, or you have admin privileges for a project on PanoramaWeb or your own instance of LabKey Server, you can browse the schema via: Admin > Go To Module > Query. Look at the details of the 'targetedms' schema.
containerPath: 'path_to_folder, // Folder of interest
queryName: 'runs', // Name of table that stores an entry for each Skyline document uploaded to the folder
Please let me know if you have any further questions, or if I can help you with any specific queries.