Having some trouble building the compiler

I checked out master and updated my Xcode to 10.2 beta 3 (10P99q), however when doing a clean build, I get the following error:

:0: error: error opening '/Users/suyashsrijan/Documents/swift-src/build/Xcode-RelWithDebInfoAssert/swift-macosx-x86_64/RelWithDebInfo/lib/swift/macosx/Swift.swiftmodule/x86_64.swiftmodule' for output: No such file or directory
:0: error: error opening '/Users/suyashsrijan/Documents/swift-src/build/Xcode-RelWithDebInfoAssert/swift-macosx-x86_64/RelWithDebInfo/lib/swift/macosx/Swift.swiftmodule/x86_64.swiftinterface' for output: No such file or directory
make: *** [/Users/suyashsrijan/Documents/swift-src/build/Xcode-RelWithDebInfoAssert/swift-macosx-x86_64/RelWithDebInfo/lib/swift/macosx/Swift.swiftmodule/x86_64.swiftmodule] Error 1

Tried re-checking out the branch (deleted the entire source directory, checked out again and ran update-checkout), but no luck. I am invoking the build script like this: ./utils/build-script -x -r --skip-build-benchmarks --clean --reconfigure

It is consistently failing on this exact step. Did something change recently?

I am on macOS 10.14.3 (18D109) if that helps!

Note: I also have this issue sometimes where if I checkout latest changes and do a build then it fails with random errors and I have to spend a lot of time trying to fix it. I would appreciate any tips here as well.

Manually creating Swift.swiftmodule and then adding a empty x86_64.swiftmodule file works (i.e. it gets replaced by the actual file(s)), however the build fails in the next phase with the same issue, but for Darwin. I guess I'll have to keep creating these directories?...

Going to try a ninja build now and see if it has the same issue.

EDIT: Ninja build works fine, seems like something's wrong with Xcode.

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