When the stack.yaml includes a dependency from github and doing stack build twice, the second command isn't a no-op despite the first command being successful. If doing stack build a third time it is, however. During the second stack build run, stack unregisters the github package saying "local file changes" and reinstalls them again. Diffing the package folder in .stack-work/downloaded before and after the second command reveals that only one file changed: downloaded/<package>/.stack-work/dist/x86_64-osx/Cabal-1.22.4.0/stack-build-cache

I can reproduce this on OS X with the following .cabal and stack.yaml content:
foobar.cabal:

name:                foobar
version:             0.1.0.0
cabal-version:       >=1.10
build-type:          Simple

library
  build-depends:
    base,
    HStringTemplate
  default-language: Haskell2010

stack.yaml:

packages:
- '.'
- location:
    git: https://github.com/factisresearch/HStringTemplate.git
    commit: 033328ce078426733020a2c0d943332f37ffee05
  extra-dep: true

extra-deps: []

resolver: lts-3.0