Where are you looking exactly in the UI for these files? Can you provide the URL of your instance and/or a screenshot?
Typically, the only thing that should ever appear in the site-level file root under the @files directory should be maintenance log files.
Files within the file repository of LabKey reside under an @files directory within the respective project or folder.
For example, if you have a project called "MyProject" and a subfolder under it called "MyFolder", your LabKey URL will look something like:
And the file repository can be viewed under:
Assuming your file's root path for your LabKey instance is called /usr/local/labkey/files, the file path on the actual server that corresponds with that filecontent page would be:
If you don't stick your files within the @files directory, LabKey will not display them to you.
Also, manually adding files via command line has some issues, such as permission problems (you should assign the same user that is running the Tomcat process to these files as the user and owner of the files). Whenever possible, it is best to use the UI to transfer files over into the LabKey file repository.
For more information about the File Repository within LabKey, please look at https://www.labkey.org/Documentation/wiki-page.view?name=files