jekyll - not processing files in subfolders

I'm using Jekyll to make a simple static site.

When I have Jekyll HTML files on the root of my project (in the same folder as the _layouts folder & config file) they render perfectly and I can preview them on http://localhost:4000/welcome.html instantly.

I'm starting to get alot of files on the root and want to organize the dynamic files into folders.

So, when I move a file into a subfolder Jekyll stops updating it. I can see my previous edits ( from when it was on the root ) but if I make any edits, it doesn't update.

http://localhost:4000/mydirec开发者_JAVA技巧tory/welcome.html - returns a 404

Should I be editing the config file to check for these folders? Something like -

source: [mydirectory1,mydirectory2]

Or am I missing something obvious?

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I assume you've run jekyll --server to check this?

I just checked my directory settings and I don't have anything in config.yaml that tell it where to look. If you run jekyll --server from the directory where you are storing everything it just recursively looks through everything and processess it according to the rules it has for each file type.

Are you running jekyll --server from the right directory?