Fix file arguments handling when using --chdir

[wata727]

Filtering issues by file arguments did not work properly with --chdir:

$ tree
.
└── subdir
    └── main.tf

1 directory, 1 file

$ tflint --chdir=subdir main.tf
Failed to parse CLI arguments; Failed to load `main.tf`: File not found

$ tflint --chdir=subdir subdir/main.tf
Cannot use --chdir and directory argument at the same time

This PR fixes this issue by parsing the arguments after the directory change. So tflint --chdir=subdir main.tf works.

This may seem counterintuitive at first glance, but in the current model where --chdir is applied first, it makes sense that the path is relative to the changed working directory.

To further prevent misunderstandings, file arguments will also be deprecated in the future. Instead, it provides an option like --filter, implying that the behavior is to filter issues after inspection of a directory, rather than inspecting only specific files.