Two things:
If these files are included in your application manifests, they are included in the siteβs application files.
In both manifestations of applications, there should be a line: require_tree , which will automatically select all your assets. Is it in these files?
Edit in response to editing:
As I structured this, there are two sets of manifestations. The standard ones (application.css / .js) are publicly available. The set of administrators is for admin pages. Include all the content you want in admin.js / .css and add these files to the precompilation array:
config.assets.precompile + = ['admin.js', 'admin.css']
This will allow you to share code between two groups. For example, you can include jquery in both, but jquery_ujs only in admin. In your admin section layout, simply include admin manifests instead of an application manifest.
In practice, you will add new files to the application or admin manifest when developing the site, and you will not have to change the configuration of the precompilation.
Once you get to adding a lot of assets, an admin section, etc., it is expected that everything will become more complex and that you should be explicit about what is included in the manifests and order (as opposed to to require_tree).
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