Problem

-- How to deploy flows in command line (for SP8 or higher)

Resolution

1- export your flow container from mapping proxy (unset the option "Deploy to Mapping Proxy")

2- modify the export to get this structure:

Resources (directory that contains the schemas if any)
Attributes.xml
BusinessDocument_1.xml
BusinessDocument_2.xml
Component.xml
Container.xml
Info.xml
MapBroker_1.xml
MapStage_1.xml
ObjectDependencies.xml
Variables.xml

3- zip the content

4- execute the following command from Interchange\tools

./mapProxyDeployer DEPLOY <directory where the zip file is located>

./mapProxyDeployer FORCE_SYNC