This looks like an issue with swift importing C modules. Debugger has that error when umbrella dir is used in modulemap i.e. In the attached package, changing

module See {
    umbrella "." // <---
    link "See"
    export *
}

to

module See {
    header "header.h"
    link "See"
    export *
}

resolves the issue.

How to reproduce?
$ unzip foo.zip && cd foo
$ xcrun --find swift
/Library/Developer/Toolchains/swift-DEVELOPMENT-SNAPSHOT-2016-11-12-a.xctoolchain/usr/bin/swift
$ swift package generate-xcodeproj
$ open foo.xcodeproj
set break point at line 4 in main.swift
run bird scheme
(lldb) po foo()
warning: Swift error in module bird.
Debug info from this module will be unavailable in the debugger.

error: in auto-import:
failed to get module 'bird' from AST context:

Changing the modulemap to use header instead of umbrella dir (and clean build) fixes the issue.

foo.zip

/cc jingham@apple.com (JIRA User)

Comment by Ryan Lovelett (JIRA)

I've experienced this with yet another configuration. Using Yams at tag 0.1.4 or commit b64e0a230dc3c4f82cac1c8c46ae3def602131f6.

If you attempt to debug a simple program, e.g.,

import Yams

let node = try Node(string: "- 1: test")
print(node)

LLDB errors with:

(lldb) po node
warning: Swift error in module sample.
Debug info from this module will be unavailable in the debugger.

warning: Swift error in module Yams.
Debug info from this module will be unavailable in the debugger.

error: in auto-import:
failed to get module 'sample' from AST context:

(lldb)

I can't reproduce it anymore. The generated framework targets in the Xcode project were kind of broken which was fixed by SR-3121 so it was probably related to that.