Documentation review and update pass to align the existing docs with the current state of the codebase

[VelmiraS]

A documentation review and update pass to align the existing docs with the current state of the codebase. This is also intended as an onboarding task — a good way for a new contributor to get familiar with the codebase while producing a concrete, useful output.

Why is this needed / describe a real-world scenario:

The documentation has accumulated inconsistencies with the actual code behavior over time. New users and contributors rely on the docs to understand how Docforge works, but misleading or outdated documentation causes confusion and incorrect usage — for example, using unsupported manifest syntax that results in parse errors, or misunderstanding how excludeFiles path matching works.

Known areas with likely inconsistencies:

• docs/manifests.md — manifest node syntax (e.g. fileTree, excludeFiles, supported forms)
• docs/manifest-ref.md — field-level reference
• docs/cmd-ref/ — CLI flags and their current defaults
• README.md — general description of what Docforge does

Task:

1. Read through all files under docs/ and README.md
2. For each documented behavior or syntax, find the corresponding implementation in the source code and verify it matches
3. For each inconsistency found, update the documentation to reflect the actual current behavior
4. Open a PR with the changes and a summary of what was corrected

This is intentionally open-ended — the goal is to find inconsistencies, not to fix a specific known list. Use the code as the source of truth.

Good first issue: This task requires reading code and writing documentation, but does not require making code changes. It is a good starting point for understanding the Docforge codebase.

/kind cleanup
/priority 3