legacy: improve script/setup

I believe the files were not cleared properly and switching between
emulator and firmware builds may have been troublesome.

Two changes:

1. `git clean` cleans only in the working tree and subdirectories.
We need to clear the related projects as well.

2. `vendor/QR-Code-generator/c/qrcodegen.{o,d}` are not git ignored
and since we use the `X` flag they are not removed. Changing to `x`,
which also removes untracked files.

legacy/script/setup

@@ -9,5 +9,5 @@ cd "$(dirname "$0")/.."
 
 script/bootstrap
 
-git clean -fdX
-git submodule foreach git clean -fdX
+git clean -fdX . ../crypto ../common ../storage
+git submodule foreach git clean -fdx