I tried to resolve module with Trouble Shooting. But it absolutely doesn't work.
./src/.flowconfig has option:
[include]
../node_modules/
I installed sequelize module and test flow:

I saw the module is installed correctly. My environment was OSX El Cap latest.
I believe the issue here is that Flow is not able to find node modules above the "root" where the .flowconfig file is. Can you move your .flowconfig up one directory?
I moved my .flowconfig file up one directory.
[2016-04-17 11:09:51] Initializing Server (This might take some time)
[2016-04-17 11:09:51] executable=/usr/local/Cellar/flow/0.22.0/bin/flow
[2016-04-17 11:09:51] version=0.22.0
[2016-04-17 11:09:51] Parsing
/Users/maniax/GameRecommend/node_modules/ No such file or directory
[2016-04-17 11:09:51] Building package heap
[2016-04-17 11:09:51] Running local inference
[2016-04-17 11:09:52] Re-resolving directly dependent files
[2016-04-17 11:09:52] Calculating dependencies
[2016-04-17 11:09:52] Merging
[2016-04-17 11:09:52] Done
[2016-04-17 11:09:52] Server is READY
[2016-04-17 11:09:52] Took 0.546391 seconds to initialize.
I removed the relative path ../node_modules -> ./node_modules. Then it worked well, but not able to resolve node_modules.
[2016-04-17 11:10:57] Initializing Server (This might take some time)
[2016-04-17 11:10:57] executable=/usr/local/Cellar/flow/0.22.0/bin/flow
[2016-04-17 11:10:57] version=0.22.0
[2016-04-17 11:10:57] Parsing
[2016-04-17 11:10:57] Building package heap
[2016-04-17 11:10:57] Running local inference
[2016-04-17 11:10:57] Re-resolving directly dependent files
[2016-04-17 11:10:57] Calculating dependencies
[2016-04-17 11:10:57] Merging
[2016-04-17 11:10:57] Done
[2016-04-17 11:10:57] Server is READY
[2016-04-17 11:10:57] Took 0.594378 seconds to initialize.
[2016-04-17 11:10:57] Status: Error
2: import Sequelize from 'sequelize';
^^^^^^^^^^^ sequelize. Required module not found
sequelize module is installed correctly. I don't know what's wrong.
I think I found my fault.
@Beingbook so, what was it?
@rmakarov94 I just added node_modules to ignore. It should place include. That was my mistake.
Most helpful comment
@rmakarov94 I just added
node_modulestoignore. It should placeinclude. That was my mistake.