apollo codegen:generate fails if there is a symlink linking to a directory

I typically have a symlink to a build directory, and have needed to remove it to run ``apollo codegen:generate``

```
$ apollo codegen:generate --target=flow
✔ Loading Apollo config
✔ Scanning for GraphQL queries (374 found)
✖ Generating query files with 'flow' target
→ EISDIR: illegal operation on a directory, read
Error: EISDIR: illegal operation on a directory, read
at inputPaths.map.inputPath (~/MyApp/node_modules/apollo-codegen-core/lib/loading.js:87:35)
at Array.map ()
at loadQueryDocuments (~/MyApp/node_modules/apollo-codegen-core/lib/loading.js:83:10)
at Object.loadAndMergeQueryDocuments (~/MyApp/node_modules/apollo-codegen-core/lib/loading.js:138:32)
at Object.generate [as default] (~/MyApp/node_modules/apollo/lib/generate.js:18:32)
at Task.task (~/MyApp/node_modules/apollo/lib/commands/codegen/generate.js:98:64)
at Promise.resolve.then.then.skipped (~/MyApp/node_modules/listr/lib/task.js:167:30)
```

Start with apollo-codegen-core/lib/loading.js around line 87, where the stack trace shows the directory symlink is being read, then inspect the codegen generate entry points in apollo/lib/generate.js and apollo/lib/commands/codegen/generate.js. Reproduce the command with a symlink to a directory and verify that code generation completes without the EISDIR error.

Written by the indexing model from the issue text.