PT-2368 - refactor all tools cli

[BON4]

Summary

This PR migrates CLI/config handling to the new Kong-based configuration layer across all affected Go tools.

The goal is to standardize flag parsing, config-file behavior, password prompts, and version/version-check flow using shared config primitives.

Changes

• Switched shared version flag to Kong-native kong.VersionFlag in lib/config/commonFlags.go.
• Migrated CLI bootstrap to config.Setup(...) in:
  • pt-mongodb-index-check
  • pt-mongodb-query-digest
  • pt-mongodb-summary
  • pt-pg-summary
  • pt-secure-collect
• Replaced legacy parsers (getopt / kingpin) with Kong struct tags and hooks (AfterApply, command Run methods).
• Unified version-check flow via config.VersionCheckFlag + versioncheck.CheckUpdates(...).
• Unified interactive secret handling via config.StdinRequestString for DB/encryption passwords.
• Refactored pt-secure-collect subcommands (collect, encrypt, decrypt, sanitize) to command structs with explicit validation and runtime handlers.

Notes

• This is primarily a CLI/config refactor; no intended functional changes in business logic.

• Main expected impact is behavior consistency across tools (flags, defaults, help/version output, password prompts).

• The contributed code is licensed under GPL v2.0

• Contributor Licence Agreement (CLA) is signed

• util/update-modules has been ran

• Documentation updated

• Test suite update