Answer by Mario Campos · Nov 30, 2012 at 01:32 PM
I contacted Squarespace Support and they provided a helpful answer, which I expanded open by organizing my scripts onto a single page:
Go to Page Settings and Disable the page [optional]
Add a Text Block
Click Files on the Link menu
You can right click and ‘Copy Link Address’ to make sure you have the correct URL
Go to your Code Injection (either the Page’s Code Injection or your site-wide Page Injection) and insert the code:
No need to link scripts via Dropbox or include the entire script in the Code Injection.
You can use this to upload any file as well, but most other things have a place (CSS files and image get uploaded in the CSS Upload File area, etc.).
Source: Creating a Text Link
Answer by Philo · Mar 24, 2016 at 07:22 PM
Didn't see it mentioned here, see details about Developer Mode on http://developers.squarespace.com/initial-setup/. Don't know when it was first made available so it may be a recent addition.
In short, squarespace offers SFTP access to the template code for your site. It also provides a GIT repo of the template code, nice!
Note: I successfully used FileZilla to establish the SFTP connection, using sftp at command line would connect but was then immediately disconnected... didn't bother investigating further to figure out what was going on.