fix: correct broken documentation links in README.md and docs/INDEX.md

[rhowardstone]

Fixes #803

Summary

This PR fixes all broken documentation links (returning 404 errors) in README.md and docs/INDEX.md by correcting paths to point to existing files in their proper subdirectories.

Problem

Issue #803 reported broken links in the documentation. Investigation revealed that many documentation files exist but are located in subdirectories, while the links pointed to the root docs/ directory.

Changes Made

README.md

• Fixed 7 broken documentation links
• Updated paths to correct subdirectory locations
• Removed references to documentation that doesn't exist yet

docs/INDEX.md

• Fixed 10+ broken documentation links
• Updated all paths to point to correct subdirectories
• Cleaned up navigation structure

Path Corrections

• docs/MCP-TOOLS.md → docs/reference/MCP_TOOLS.md
• docs/AGENT-SYSTEM.md → docs/reference/AGENTS.md
• docs/SPARC.md → docs/reference/SPARC.md
• docs/API_DOCUMENTATION.md → docs/api/API_DOCUMENTATION.md
• docs/ARCHITECTURE.md → docs/architecture/ARCHITECTURE.md
• docs/DEPLOYMENT.md → docs/development/DEPLOYMENT.md
• docs/DEVELOPMENT_WORKFLOW.md → docs/development/DEVELOPMENT_WORKFLOW.md

Testing

• Verified all updated links point to existing files
• Checked that removed links reference non-existent documentation
• No functional changes - documentation links only

Notes

• Clean fix with no TODO comments or placeholder code
• Follows existing documentation structure
• Maintains readability and user experience

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