Flow doesn't see external modules, starting with 0.46

Flow stopped seeing external modules with 0.46

Replicate this issue:

package.json:

````json
{
"name": "flow_min_case",
"version": "1.0.0",
"main": "src/index.js",
"license": "MIT",
"dependencies": {
"emoji-poop": "^1.3.0"
}
}
````

src/index.js:

````js
/* @flow */
import emoji from 'emoji-poop';
````

src/.flowconfig:

````
[ignore]

[include]
../node_modules/emoji-poop

[libs]

[options]
````

1. `npm install` (or `yarn`)
2. `cd src && flow check`

````
index.js:2
2: import emoji from 'emoji-poop';
^^^^^^^^^^^^ emoji-poop. Required module not found

Found 1 error
````

checking works with 0.45 and lower. With 0.46 and above, it shows the error. ~~~I haven't yet tried to build from master, so I am not sure if it's present there.~~~ It has the same error in master, too.