Move patches to patches/, and change how secret symbols work

[Rangi42]

When I run this locally I no longer get the green current-line highlight, but I can't tell why.

It changes the secret symbols to use a ~~SEC_ prefix instead of __SEC_ so that they can't accidentally (or on-purpose) be aliased by actual labels (e.g. __SEC_2_3_main.asm is a valid name for a local label).