Missing CLI flags for some configuration options

[massdo]

Hi @yamadashy ! 👋

Description

While analyzing the correspondence between CLI flags and configuration options, I noticed that some configuration fields don't have corresponding CLI flags. I'd like to know if this is intentional or if we should add them for consistency.

Current missing CLI flags for existing config options:

• output.headerText -> add --header-text ?
• output.instructionFilePath -> add--instruction-file ?
• output.includeEmptyDirectories -> add --include-empty-directories ?
• ignore.useGitignore -> add --no-gitignore ?
• ignore.useDefaultPatterns -> add --no-default-patterns ?

Use Case

I specifically need these CLI flags for the Repomix Runner VS Code extension. Currently, the extension passes VS Code configuration to Repomix through CLI flags.

I'd be happy to submit a PR to add them if you don't have time.

[yamadashy]

Hi, @massdo !
Thank you for the suggestion!
I initially only added CLI flags for commonly used options, but you make a great point - having CLI flags for all config options improves usability, especially for tool integrations and npm scripts. Having consistent CLI flags for all config options makes it more flexible and user-friendly.

The proposed flags look good! I'd be very grateful if you could submit a PR!

One implementation note:
Due to Commander.js's behavior, flags with --no- prefix are passed to the opposite name. For example, --no-security-check is passed as securityCheck: false.

Thank you again for your continued contributions to Repomix!