feat: replace run.skip-xxx options by issues.exclude-xxx options

[ldez]

The option name skip-xxx is a source of confusion.
And to increase the confusion, those options are inside the section run.

This sample of issues illustrate the problem: #1912, #2748, #4084, #3775, #1832, #4360

My proposal is move and rename those options:

• run.skip-dirs deprecation: replaced by issues.exclude-dirs
• run.skip-dirs-use-default deprecation: replaced by issues.exclude-dirs-use-default
• run.skip-files deprecation: replaced by issues.exclude-files

This is a non-breaking change: the skip-xxx will still work but with a warning, and issues.exclude-xxx options do the same things as skip-xxx.

log output

Using a flag:

$ go run ./cmd/golangci-lint run --skip-dirs=foo
Flag --skip-dirs has been deprecated, check the documentation for more information.
WARN [config_reader] The configuration option `run.skip-dirs` is deprecated, please use `issues.exclude-dirs`. 

Using the file:

$ go run ./cmd/golangci-lint run
WARN [config_reader] The configuration option `run.skip-dirs` is deprecated, please use `issues.exclude-dirs`. 

one commit, one change.