Fix potential bugs

When specifying packages in command line, the install spec in config file
needs also be respected.
Merge branch 'develop'
Merge branch 'develop'
Merge branch 'develop'
Minor refactor
Refactor codes

Parallel netcdf-fortran in Mac is failed to build, tell users this problem.

Collect package codes into framework/package directory.

Add report subcommand, but not implemented anything.

Add package name BASH autocompletion.
Merge branch 'release/1.0.0-a1' into develop