I’ve never been happy with any engine I’ve come across so I too make almost everything from scratch. External libraries I use is for the asset compiler for loading images and fonts.

I program in C++ with some custom language extensions.

By making the tech yourself you can custom tailor it to your needs and add features like:

• asset hot-reloading,
• code hot-reloading,
• reflection (mostly useful for debugging purposes),
• config system,
• type safe shader invocations (no more accidentally writing wrong vertex type),
• etc.

I never liked any scripting languages so I stick with C++ for game logic as well.

I don’t know if there is a single book that would cover indie game development. But here are some suggestions on various game development topics:

• Game Engine Architecture
  • Mostly of value if you’re planning on creating your own tech rather than an off-the-shelf engine.
• The Book of Shaders
  • An “interactive web book” covering a bunch of shader techniques.
• Rules of Play: Game Design Fundamentals
  • I haven’t read this one myself but heard good things about it.
• Pixel Logic
  • In-depth tutorials for pixel art creation, but also touches on other game art areas.

Of course what to read up on depends on what kind of games you’re making, but the above should cover at least the basics.