Installing documentation with npm v1 or v2 yields a gigantic `node_modules`

Unfortunately, we need to recommend: use yarn or npm v3 to install documentation. npm v1 and v2 are unable to properly de-duplicate dependencies, so they will create wastefully large node_modules directories under documentation.

documentation is inferring too much about my code

If you've written very dynamic JavaScript, all of documentation's intelligence might not understand it. If:

documentation is wrong in a clear way, please open a descriptive issue with a code snippet and we can help!
if it's right technically but you want to control your docs entirely, use the @name tag to declare the name of the thing (function, variable, etc) you're referring to, and the tool will not try to infer anything at all.

Error: watch ENOSPC

Linux systems can have a low limit of 'watchable files'. To increase this limit, follow the advice in this StackOverflow answer.

Error: EMFILE: too many open files

You'll need to increase the ulimit maximum for your system: here's a StackOverflow issue explaining how.