Right side navigation lists modules correctly. Main body lists all modules as External modules. See below screen shot.

Hi, thank you for your message. Looks like this a naming confusion.
The separation of code belonging to your project ("Internals") and vendor / lib code ("Externals") only appears in the right side navigation and not within the content - this is intentional. You configure this two groups using the --externalPattern option, they are not code related.
Within the left side the caption "External modules" means "CommonJS / AMD modules", the addition "External" was necessary as TypeScript also has "modules" which are basically object literals. These two will be renamed in the near future and will show up as "modules" and "namespaces", see #109.
However I'm not happy with the titles in the right side navigation, maybe we should remove "Internals" altogether and rename "Externals" to something like "Vendors" or "Libs"?
I like the idea of naming the "Externals" to "Libs"
I'd suggest using "Dependencies" and remove "internal" (or "Internals") at all - they are not internals they are just the lib.
Ran into this today, and spent an hour trying different externalPattern combinations to no avail, so I figure that this is the issue.
Is this a theme issue, or a core issue?
@balupton Internal/external is a core dis tinction. You may want to look at #903 or the internal-external plugin. You can also ask questions on gitter if that is more helpful.
From what that plugin says:
Typedoc uses the files: [] array (in tsconfig.json) to determine if code is "Internal". If a file being parsed is in the files: [] array, then the code in that file is "Internal".
Seems like typedoc is ignoring the includes property of tsconfig.json, which should get the same (internal) treatment as the files property.
If you are using a jsconfig.json file TypeDoc will not look at it so you will need to pass those file/directories to typedoc explicitly. Only tsconfig.json files are read.
Most helpful comment
I'd suggest using "Dependencies" and remove "internal" (or "Internals") at all - they are not internals they are just the lib.