refactor(docs): normalize documentation naming to lowercase for PEP8 compliance (#434)

* refactor(docs): rename directories to lowercase for PEP8 compliance

- Developer-Guide → developer-guide
- Getting-Started → getting-started
- Reference → reference
- Templates → templates
- User-Guide → user-guide
- User-Guide-jp → user-guide-jp
- User-Guide-kr → user-guide-kr
- User-Guide-zh → user-guide-zh

This change aligns with Python PEP8 package naming conventions.
All 43 files affected.

* refactor: rename root documentation files to lowercase

- CHANGELOG.md → changelog.md
- CODE_OF_CONDUCT.md → code_of_conduct.md
- CONTRIBUTING.md → contributing.md
- SECURITY.md → security.md

Aligns with Python package naming conventions (PEP8).
README files remain uppercase as per convention.

* refactor: move documentation files to docs/ for cleaner root

Moved OSS standard files to docs/:
- CHANGELOG.md → docs/CHANGELOG.md
- CODE_OF_CONDUCT.md → docs/CODE_OF_CONDUCT.md
- CONTRIBUTING.md → docs/CONTRIBUTING.md
- SECURITY.md → docs/SECURITY.md

Root now contains only essential files:
✓ README files (表紙: en, ja, kr, zh)
✓ LICENSE (法的要件)
✓ Build configs (pyproject.toml, setup.py, MANIFEST.in)
✓ VERSION

Rationale:
Cleaner root structure following modern Python project conventions.
All detailed documentation consolidated in docs/ directory.

* refactor: update documentation links after restructure

Auto-updated internal documentation links to reflect new structure:
- docs/ subdirectories now lowercase (PEP8)
- Root files moved to docs/
- All cross-references updated

This commit includes linter-generated link updates.

* chore(docs): keep OSS-standard uppercase root files (CHANGELOG, CODE_OF_CONDUCT, CONTRIBUTING, SECURITY)

* chore(docs): remove duplicated PR docs from repo root (moved under docs)

* docs: rename pm-agent-implementation-status.md -> PM_AGENT.md for clarity

* docs: update links to PM_AGENT.md after rename

---------

Co-authored-by: kazuki <kazuki@kazukinoMacBook-Air.local>

README.md

@@ -392,51 +392,51 @@ The Deep Research system intelligently coordinates multiple tools:
 <tr>
 <td valign="top">
 
-- 📝 [**Quick Start Guide**](docs/Getting-Started/quick-start.md)  
+- 📝 [**Quick Start Guide**](docs/getting-started/quick-start.md)  
   *Get up and running fast*
 
-- 💾 [**Installation Guide**](docs/Getting-Started/installation.md)  
+- 💾 [**Installation Guide**](docs/getting-started/installation.md)  
   *Detailed setup instructions*
 
 </td>
 <td valign="top">
 
-- 🎯 [**Commands Reference**](docs/User-Guide/commands.md)  
+- 🎯 [**Commands Reference**](docs/user-guide/commands.md)  
   *All 25 slash commands*
 
-- 🤖 [**Agents Guide**](docs/User-Guide/agents.md)  
+- 🤖 [**Agents Guide**](docs/user-guide/agents.md)  
   *15 specialized agents*
 
-- 🎨 [**Behavioral Modes**](docs/User-Guide/modes.md)  
+- 🎨 [**Behavioral Modes**](docs/user-guide/modes.md)  
   *7 adaptive modes*
 
-- 🚩 [**Flags Guide**](docs/User-Guide/flags.md)  
+- 🚩 [**Flags Guide**](docs/user-guide/flags.md)  
   *Control behaviors*
 
-- 🔧 [**MCP Servers**](docs/User-Guide/mcp-servers.md)  
+- 🔧 [**MCP Servers**](docs/user-guide/mcp-servers.md)  
   *7 server integrations*
 
-- 💼 [**Session Management**](docs/User-Guide/session-management.md)  
+- 💼 [**Session Management**](docs/user-guide/session-management.md)  
   *Save & restore state*
 
 </td>
 <td valign="top">
 
-- 🏗️ [**Technical Architecture**](docs/Developer-Guide/technical-architecture.md)  
+- 🏗️ [**Technical Architecture**](docs/developer-guide/technical-architecture.md)  
   *System design details*
 
-- 💻 [**Contributing Code**](docs/Developer-Guide/contributing-code.md)  
+- 💻 [**Contributing Code**](docs/developer-guide/contributing-code.md)  
   *Development workflow*
 
-- 🧪 [**Testing & Debugging**](docs/Developer-Guide/testing-debugging.md)  
+- 🧪 [**Testing & Debugging**](docs/developer-guide/testing-debugging.md)  
   *Quality assurance*
 
 </td>
 <td valign="top">
-- 📓 [**Examples Cookbook**](docs/Reference/examples-cookbook.md)  
+- 📓 [**Examples Cookbook**](docs/reference/examples-cookbook.md)  
   *Real-world recipes*
 
-- 🔍 [**Troubleshooting**](docs/Reference/troubleshooting.md)  
+- 🔍 [**Troubleshooting**](docs/reference/troubleshooting.md)  
   *Common issues & fixes*
 
 </td>