> When you need to fix a toilet you don't usually start with learning hydrodynamics.

I think that's wrong. You weren't taught hydrodynamics. You were taught how a toilet works and then ran in to a plumbing problem. The issue is there isn't much out there on plumbing, so to speak. It reminds me of The Cliff of Confusion and The Desert of Despair.[0]

There's tons of hand-holding tutorials that will teach you the basic syntax of JavaScript or PHP, but once you're set loose in to the real world, where we're no longer just reversing strings and other trivial exercises, there's surprisingly few tutorials available (I suspect because it's way easier to write about simple facts than it is opinionated best practices, but that's a different topic...)

I don't really have any silver-bullet for you here. The "knowing libraries, how to run php on my system, a bunch of php specific stuff" part is mostly a matter of tenacity, Googling, and reading tons of dry technical documentation. It takes a while before the big picture starts to click.

[0] http://www.vikingcodeschool.com/posts/why-learning-to-code-i...