chore(doc): align documentation structure and fix validation errors

[sonesuke]

Walkthrough - Aligning Docgraph Requirements

I have aligned the documentation structure with the updated docgraph.toml rules and resolved all linting errors.

Changes

1. Configuration Updates (docgraph.toml)

• Corrected Directions: Flipped relationship directions from from to to for FR, NFR, MOD, ACT, IF, and ADR to match the document structure (outgoing links).
• New Rules: Added missing rules for UC to link to ACT, IF, and FR. Added rule for FR to reference IF. Added rule for CC to link to ADR.
• Targets: Updated NFR to constrain CC.

2. Template Refinements

• Standardized Headers: Updated doc/templates/constraint.md to use H2 headers (## {Name}) instead of expecting H1/H2 mix.
• Optional Descriptions: Updated module.md, usecases.md, non-functional.md, and cross-cutting.md to match patterns with optional descriptions (e.g., [* (*)](*#*) {description}).
• Wildcard Fix: Corrected usecases.md pattern from *#*_ to *#* to correctly match node IDs like ACT_CI.

3. Content Updates

• Modules (module.md): Populated empty Realizes sections in sub-modules (MOD_CORE_RULES, MOD_CORE_GRAPH, MOD_LSP_SERVER) with relevant functional requirement links.
• Constraints:
  • Updated development.md to remove the top-level H1 header and use H2 headers for all nodes, matching the new template.
  • Updated quality.md to use H2 header.
• Cross-cutting Concepts:
  • Updated thin-handlers.md, dependency-rule.md, etc., to match the new template structure (moved Decided by before Reflected in).
  • Removed empty Reflected in lists where appropriate.
• Use Cases: Added Actors and Interfaces sections to ci.md.
• Link Text: Fixed DG004 errors in lsp.md and module.md.

Verification Results

Automated Checks

• docgraph check passed with 0 errors.
• docgraph graph generated the dependency graph successfully.