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"all: true" ignores include flag #782

Description

@jwalton

Expected Behavior

With this config file:

{
    "require": ["babel-register"],
    "reporter": ["lcov", "text-summary"],
    "extension": [".jsx", "*.js"],
    "include": ["src/**"],
    "all": true,
    "sourceMap": false,
    "instrument": false
}

I would expect only files in the 'src' folder to be instrumented.

Observed Behavior

In my project, I see nyc run out of memory because it tries to instrument everything. If I add a console.log() to this line I see that webpack built files in /dist are being instrumented.

Forensic Information

Operating System: OS/X
Environment Information:
node: 8.9.4
nyc: 11.4.1
output: https://gist.github.com/jwalton/193c1fcd02ad861d8805047e193b93f0

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