The standard behaviour for the Meterian client is to consider the folder where it's pointed to a project. It will look for any (supported) manifest files in such folder and will activate automatically the correct analyzers. The inner folder structure is indeed opaque to the scanner, which relies on the declarations in the manifest files themselves.
Some analyzers, however, can also work recursively, looking into subfolders of the current folder. This happens with Java/Ant, Dotnet, and NodeJS. This behaviour can be controlled across all scanners that are using it providing a set of excluded folders that such analyzers will not visit, using the parameter
--exclude-folders as in this example:
** works across directories, while
* is the general wildcard.
This options allows to exclude multiple paths by separating them with a comma as in the example