x/tools: various test failures in TryBot run

[toothrot]

What version of Go are you using (go version)?

https://golang.org/cl/216158

$ go tip

Does this issue reproduce with the latest release?

Doesn't seem to reproduce consistently, possibly flaky tests

What operating system and processor architecture are you using (go env)?

go env Output

$ go env

What did you do?

Ran trybots: https://storage.googleapis.com/go-build-log/2c418b7c/linux-amd64_209916fd.log

What did you expect to see?

Success

What did you see instead?

2020/01/24 15:23:15 no dep handle: no metadata for nosuchpkg
	package = nosuchpkg
2020/01/24 15:23:15 no dep handle: no metadata for golang.org/x/tools/internal/lsp/protocol
	package = golang.org/x/tools/internal/lsp/protocol
2020/01/24 15:23:15 no dep handle: no metadata for golang.org/x/xerrors
	package = golang.org/x/xerrors
2020/01/24 15:23:20 no dep handle: no metadata for nosuchpkg
	package = nosuchpkg
2020/01/24 15:23:20 no dep handle: no metadata for golang.org/x/tools/internal/lsp/protocol
	package = golang.org/x/tools/internal/lsp/protocol
2020/01/24 15:23:20 no dep handle: no metadata for golang.org/x/xerrors
	package = golang.org/x/xerrors
--- FAIL: TestModfileSuggestedFixes (0.48s)
    --- FAIL: TestModfileSuggestedFixes/indirect (0.35s)
        lsp_test.go:977: err: exit status 2: stderr: flag provided but not defined: -modfile
            usage: go mod tidy [-v]
            Run 'go help mod tidy' for details.
            
    --- FAIL: TestModfileSuggestedFixes/unused (0.14s)
        lsp_test.go:977: err: exit status 2: stderr: flag provided but not defined: -modfile
            usage: go mod tidy [-v]
            Run 'go help mod tidy' for details.
FAIL
FAIL	golang.org/x/tools/internal/lsp	9.074s

--- FAIL: TestDiagnostics (1.71s)
    --- FAIL: TestDiagnostics/indirect (0.40s)
        mod_test.go:155: err: exit status 2: stderr: flag provided but not defined: -modfile
            usage: go mod tidy [-v]
            Run 'go help mod tidy' for details.
            
    --- FAIL: TestDiagnostics/unused (0.29s)
        mod_test.go:155: err: exit status 2: stderr: flag provided but not defined: -modfile
            usage: go mod tidy [-v]
            Run 'go help mod tidy' for details.
            
    --- FAIL: TestDiagnostics/invalidrequire (0.42s)
        mod_test.go:155: err: exit status 2: stderr: flag provided but not defined: -modfile
            usage: go mod tidy [-v]
            Run 'go help mod tidy' for details.
            
    --- FAIL: TestDiagnostics/invalidgo (0.36s)
        mod_test.go:155: err: exit status 2: stderr: flag provided but not defined: -modfile
            usage: go mod tidy [-v]
            Run 'go help mod tidy' for details.
            
    --- FAIL: TestDiagnostics/unknowndirective (0.23s)
        mod_test.go:155: err: exit status 2: stderr: flag provided but not defined: -modfile
            usage: go mod tidy [-v]
            Run 'go help mod tidy' for details.
            
FAIL
FAIL	golang.org/x/tools/internal/lsp/mod	1.996s

--- FAIL: TestInvalidFilesInOverlay (7.21s)
    --- FAIL: TestInvalidFilesInOverlay/GOPATH (2.88s)
        --- FAIL: TestInvalidFilesInOverlay/GOPATH/test_variant (2.80s)
            packages114_test.go:71: 0. d.D: got unknown, want "GET_test"
        --- FAIL: TestInvalidFilesInOverlay/GOPATH/second_file (0.07s)
            packages114_test.go:71: 1. d.D: got unknown, want "GET_util"
    --- FAIL: TestInvalidFilesInOverlay/Modules (4.33s)
        --- FAIL: TestInvalidFilesInOverlay/Modules/test_variant (4.13s)
            packages114_test.go:71: 0. d.D: got unknown, want "GET_test"
        --- FAIL: TestInvalidFilesInOverlay/Modules/second_file (0.18s)
            packages114_test.go:71: 1. d.D: got unknown, want "GET_util"
FAIL
FAIL	golang.org/x/tools/go/packages	67.514s

Are these flaky?

/cc @stamblerre