claude-code-ultimate-guide-mcp 1.0.3 → 1.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. package/content/llms.txt +96 -150
  2. package/content/reference.yaml +161 -161
  3. package/dist/index.js +578 -5
  4. package/package.json +1 -1
package/content/reference.yaml CHANGED
@@ -9,7 +9,7 @@ updated: "2026-02-26"
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  # ════════════════════════════════════════════════════════════════
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  # DEEP DIVE - Line numbers in guide/ultimate-guide.md
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  # Usage: Read file at line N for detailed documentation on topic
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- # For architecture internals, see guide/architecture.md
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+ # For architecture internals, see guide/core/architecture.md
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  # ════════════════════════════════════════════════════════════════
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  deep_dive:
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  # Visual Diagrams Series (40 Mermaid diagrams)
@@ -22,11 +22,11 @@ deep_dive:
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  exploration_workflow: "guide/workflows/exploration-workflow.md"
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  script_generation: "guide/workflows/iterative-refinement.md:200"
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  anti_anchoring_prompts: "examples/semantic-anchors/anchor-catalog.md:248"
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- session_limits: "guide/architecture.md:442"
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+ session_limits: "guide/core/architecture.md:442"
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  claudemd_sizing: 3054
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- scope_success_rates: "guide/adoption-approaches.md:26"
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+ scope_success_rates: "guide/roles/adoption-approaches.md:26"
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  # Claude Code Releases
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- claude_code_releases: "guide/claude-code-releases.md"
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+ claude_code_releases: "guide/core/claude-code-releases.md"
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  claude_code_releases_yaml: "machine-readable/claude-code-releases.yaml"
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  # Code Review Automation (Pat Cullen, Jan 2026)
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  review_pr_advanced: "examples/commands/review-pr.md:81"
@@ -58,29 +58,29 @@ deep_dive:
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  team_ai_instructions_token_savings: "59% context token reduction (measured, 5-dev team)"
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  team_ai_instructions_threshold: "Team 5+ devs with multiple AI tools"
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  # Known Issues & Critical Bugs (verified community reports)
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- known_issues: "guide/known-issues.md"
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- known_issues_github_bug: "guide/known-issues.md:7" # GitHub auto-creation bug
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- known_issues_token_consumption: "guide/known-issues.md:105" # Excessive token usage
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- known_issues_model_quality_aug2025: "guide/known-issues.md:197" # Resolved: Aug 2025 degradation
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+ known_issues: "guide/core/known-issues.md"
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+ known_issues_github_bug: "guide/core/known-issues.md:7" # GitHub auto-creation bug
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+ known_issues_token_consumption: "guide/core/known-issues.md:105" # Excessive token usage
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+ known_issues_model_quality_aug2025: "guide/core/known-issues.md:197" # Resolved: Aug 2025 degradation
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  # Template Installation
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  install_templates_script: "scripts/install-templates.sh"
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  # Session management
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- session_search: "guide/observability.md:38"
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+ session_search: "guide/ops/observability.md:38"
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  session_search_script: "examples/scripts/session-search.sh"
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  cc_sessions_script: "examples/scripts/cc-sessions.py"
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- session_resume_limitations: "guide/observability.md:126"
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- session_cross_folder_migration: "guide/observability.md:126"
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- session_migration_manual: "guide/observability.md:126"
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- session_migration_risks: "guide/observability.md:126"
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- session_migration_community_tool: "guide/observability.md:52"
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+ session_resume_limitations: "guide/ops/observability.md:126"
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+ session_cross_folder_migration: "guide/ops/observability.md:126"
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+ session_migration_manual: "guide/ops/observability.md:126"
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+ session_migration_risks: "guide/ops/observability.md:126"
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+ session_migration_community_tool: "guide/ops/observability.md:52"
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  session_migration_issue: "https://github.com/anthropics/claude-code/issues/1516"
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  session_migration_weller_skill: "https://github.com/jimweller/dotfiles/tree/main/dotfiles/claude-code/skills/claude-migrate-session"
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  # Activity monitoring
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- activity_monitoring: "guide/observability.md:467" # Tool call audit via JSONL
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- activity_monitoring_queries: "guide/observability.md:467" # jq queries for audit
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- activity_monitoring_alerts: "guide/observability.md:467" # Sensitive pattern detection
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- external_monitoring_tools: "guide/observability.md:527" # ccusage, claude-code-otel, Akto, MLflow, ccboard
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- proxying_claude_code: "guide/observability.md:699" # Proxyman, mitmproxy, ANTHROPIC_API_URL
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+ activity_monitoring: "guide/ops/observability.md:467" # Tool call audit via JSONL
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+ activity_monitoring_queries: "guide/ops/observability.md:467" # jq queries for audit
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+ activity_monitoring_alerts: "guide/ops/observability.md:467" # Sensitive pattern detection
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+ external_monitoring_tools: "guide/ops/observability.md:527" # ccusage, claude-code-otel, Akto, MLflow, ccboard
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+ proxying_claude_code: "guide/ops/observability.md:699" # Proxyman, mitmproxy, ANTHROPIC_API_URL
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  ccboard_activity_plan: "docs/resource-evaluations/ccboard-activity-module-plan.md"
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  # Cost optimization - Local execution bridge
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  bridge_script: "examples/scripts/bridge.py"
@@ -91,7 +91,7 @@ deep_dive:
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  rtk_website: "https://www.rtk-ai.app/"
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  rtk_evaluation: "docs/resource-evaluations/rtk-evaluation.md"
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  rtk_guide: "guide/ultimate-guide.md:14553"
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- rtk_third_party: "guide/third-party-tools.md:7"
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+ rtk_third_party: "guide/ecosystem/third-party-tools.md:7"
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  rtk_claude_md: "examples/claude-md/rtk-optimized.md"
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  rtk_skill: "examples/skills/rtk-optimizer/SKILL.md"
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  rtk_hook: "examples/hooks/bash/rtk-auto-wrapper.sh"
@@ -100,7 +100,7 @@ deep_dive:
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  rtk_score: "5/5"
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  rtk_installation: "cargo install rtk or brew install rtk-ai/tap/rtk"
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  # Google Antigravity (Agent-First IDE)
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- antigravity_guide: "guide/ai-ecosystem.md:1366"
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+ antigravity_guide: "guide/ecosystem/ai-ecosystem.md:1366"
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  antigravity_evaluation: "docs/resource-evaluations/google-antigravity-evaluation.md"
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  antigravity_proxy: "https://www.npmjs.com/package/antigravity-claude-proxy"
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  antigravity_codelabs: "https://codelabs.developers.google.com/getting-started-google-antigravity"
@@ -125,35 +125,35 @@ deep_dive:
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  talk_pipeline_patterns: "skill chaining + file-based state + tool permission scoping + human-in-the-loop gate + AI-to-AI handoff (Claude → Kimi)"
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  talk_pipeline_checkpoint: "Stage 4 CHECKPOINT: user selects angle + title before script starts"
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  talk_pipeline_kimi: "kimi.com (free) — copy-paste Stage 5 prompt for AI slide generation"
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- # reMarkable 2 + AI (guide/remarkable-ai.md)
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- remarkable_ai_guide: "guide/remarkable-ai.md"
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- remarkable_mcp_server: "guide/remarkable-ai.md#1-remarkable-mcp--le-game-changer"
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+ # reMarkable 2 + AI (guide/ecosystem/remarkable-ai.md)
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+ remarkable_ai_guide: "guide/ecosystem/remarkable-ai.md"
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+ remarkable_mcp_server: "guide/ecosystem/remarkable-ai.md#1-remarkable-mcp--le-game-changer"
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  remarkable_mcp_repo: "https://github.com/SamMorrowDrums/remarkable-mcp"
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- remarkable_ghostwriter: "guide/remarkable-ai.md#2-ghostwriter--interface-vision-llm"
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- remarkable_obsidian_sync: "guide/remarkable-ai.md#3-sync-remarkable--obsidian"
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- remarkable_ocr_pipeline: "guide/remarkable-ai.md#4-ocr--ai-pipeline-custom"
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- remarkable_ssh_tools: "guide/remarkable-ai.md#5-accès-ssh-et-outils-communautaires"
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- remarkable_meeting_workflow: "guide/remarkable-ai.md#10-meeting-notes--ai-summary"
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- remarkable_workflows_to_build: "guide/remarkable-ai.md#14-workflows-ai-augmentés-à-construire"
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- remarkable_getting_started: "guide/remarkable-ai.md#15-par-où-commencer"
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+ remarkable_ghostwriter: "guide/ecosystem/remarkable-ai.md#2-ghostwriter--interface-vision-llm"
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+ remarkable_obsidian_sync: "guide/ecosystem/remarkable-ai.md#3-sync-remarkable--obsidian"
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+ remarkable_ocr_pipeline: "guide/ecosystem/remarkable-ai.md#4-ocr--ai-pipeline-custom"
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+ remarkable_ssh_tools: "guide/ecosystem/remarkable-ai.md#5-accès-ssh-et-outils-communautaires"
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+ remarkable_meeting_workflow: "guide/ecosystem/remarkable-ai.md#10-meeting-notes--ai-summary"
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+ remarkable_workflows_to_build: "guide/ecosystem/remarkable-ai.md#14-workflows-ai-augmentés-à-construire"
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+ remarkable_getting_started: "guide/ecosystem/remarkable-ai.md#15-par-où-commencer"
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  remarkable_community: "https://github.com/reHackable/awesome-reMarkable"
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  # Whitepapers (FR + EN) — 9 focused whitepapers on Claude Code
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  whitepapers_url: "https://www.florian.bruniaux.com/guides"
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  whitepapers_fr: "whitepapers/fr/" # FR sources (Quarto .qmd)
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  whitepapers_en: "whitepapers/en/" # EN sources (Quarto .qmd)
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  whitepapers_topics: "foundations, prompting, customization, security, architecture, team, privacy, reference, agent-teams"
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- # Learning with AI (guide/learning-with-ai.md)
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- learning_quick_check: "guide/learning-with-ai.md:38"
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- learning_uval_protocol: "guide/learning-with-ai.md:218"
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- learning_claude_config: "guide/learning-with-ai.md:458"
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- learning_breaking_dependency: "guide/learning-with-ai.md:575"
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- learning_embracing_ai: "guide/learning-with-ai.md:623"
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- learning_30day_plan: "guide/learning-with-ai.md:815"
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- learning_red_flags: "guide/learning-with-ai.md:612"
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+ # Learning with AI (guide/roles/learning-with-ai.md)
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+ learning_quick_check: "guide/roles/learning-with-ai.md:38"
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+ learning_uval_protocol: "guide/roles/learning-with-ai.md:218"
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+ learning_claude_config: "guide/roles/learning-with-ai.md:458"
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+ learning_breaking_dependency: "guide/roles/learning-with-ai.md:575"
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+ learning_embracing_ai: "guide/roles/learning-with-ai.md:623"
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+ learning_30day_plan: "guide/roles/learning-with-ai.md:815"
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+ learning_red_flags: "guide/roles/learning-with-ai.md:612"
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  # Productivity Research RCTs
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- productivity_rct_metr: "guide/learning-with-ai.md:925" # METR 2025: experienced devs 19% slower on large codebases despite perceiving 20% faster
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- productivity_rct_echoes: "guide/learning-with-ai.md:926" # Borg 2025: 30.7% faster (median), ~55.9% habitual users, no maintainability impact downstream
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- productivity_maintainability_empirical: "guide/learning-with-ai.md:926" # Empirical data on "AI code is unmaintainable" claim — blind RCT shows no significant difference
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+ productivity_rct_metr: "guide/roles/learning-with-ai.md:925" # METR 2025: experienced devs 19% slower on large codebases despite perceiving 20% faster
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+ productivity_rct_echoes: "guide/roles/learning-with-ai.md:926" # Borg 2025: 30.7% faster (median), ~55.9% habitual users, no maintainability impact downstream
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+ productivity_maintainability_empirical: "guide/roles/learning-with-ai.md:926" # Empirical data on "AI code is unmaintainable" claim — blind RCT shows no significant difference
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  trust_calibration_maintainability_nuance: "guide/ultimate-guide.md:1097" # Nuance: defect rates ≠ maintenance burden (Borg et al. 2025)
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  learning_mode_template: "examples/claude-md/learning-mode.md"
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  learn_quiz_command: "examples/commands/learn/quiz.md"
@@ -161,23 +161,23 @@ deep_dive:
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  learn_alternatives_command: "examples/commands/learn/alternatives.md"
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  learning_capture_hook: "examples/hooks/bash/learning-capture.sh"
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  # Anti-patterns
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- vibe_coding_trap: "guide/learning-with-ai.md:87"
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+ vibe_coding_trap: "guide/roles/learning-with-ai.md:87"
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  vibe_coding_context_overload: 13097
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  vibe_coding_context_overload_source: "Jens Rusitschka, 'Vibe Coding, Level 2' (Jan 2026)"
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  vibe_coding_phased_strategy: 13097
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- # AI Traceability & Attribution (guide/ai-traceability.md) - Added 2026-01-24
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- ai_traceability_guide: "guide/ai-traceability.md"
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- ai_traceability_why: "guide/ai-traceability.md:29"
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- ai_traceability_disclosure_spectrum: "guide/ai-traceability.md:64"
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- ai_traceability_co_authored_by: "guide/ai-traceability.md:98"
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- ai_traceability_assisted_by: "guide/ai-traceability.md:120"
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- ai_traceability_git_ai: "guide/ai-traceability.md:170"
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- ai_traceability_llvm_policy: "guide/ai-traceability.md:201"
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- ai_traceability_ghostty_policy: "guide/ai-traceability.md:236"
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- ai_traceability_fedora_policy: "guide/ai-traceability.md:261"
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- ai_traceability_promptpwnd: "guide/ai-traceability.md:501"
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- ai_traceability_implementation: "guide/ai-traceability.md:566"
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- ai_traceability_templates: "guide/ai-traceability.md:648"
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+ # AI Traceability & Attribution (guide/ops/ai-traceability.md) - Added 2026-01-24
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+ ai_traceability_guide: "guide/ops/ai-traceability.md"
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+ ai_traceability_why: "guide/ops/ai-traceability.md:29"
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+ ai_traceability_disclosure_spectrum: "guide/ops/ai-traceability.md:64"
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+ ai_traceability_co_authored_by: "guide/ops/ai-traceability.md:98"
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+ ai_traceability_assisted_by: "guide/ops/ai-traceability.md:120"
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+ ai_traceability_git_ai: "guide/ops/ai-traceability.md:170"
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+ ai_traceability_llvm_policy: "guide/ops/ai-traceability.md:201"
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+ ai_traceability_ghostty_policy: "guide/ops/ai-traceability.md:236"
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+ ai_traceability_fedora_policy: "guide/ops/ai-traceability.md:261"
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+ ai_traceability_promptpwnd: "guide/ops/ai-traceability.md:501"
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+ ai_traceability_implementation: "guide/ops/ai-traceability.md:566"
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+ ai_traceability_templates: "guide/ops/ai-traceability.md:648"
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  # AI Disclosure Templates
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  ai_disclosure_contributing: "examples/config/CONTRIBUTING-ai-disclosure.md"
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  ai_disclosure_pr_template: "examples/config/PULL_REQUEST_TEMPLATE-ai.md"
@@ -187,15 +187,15 @@ deep_dive:
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  tts_voice_catalog: "examples/integrations/agent-vibes/voice-catalog.md"
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  tts_troubleshooting: "examples/integrations/agent-vibes/troubleshooting.md"
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  tts_workflow: "guide/workflows/tts-setup.md"
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- tts_ai_ecosystem: "guide/ai-ecosystem.md:1124"
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+ tts_ai_ecosystem: "guide/ecosystem/ai-ecosystem.md:1124"
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  tts_hook_example: "examples/hooks/bash/tts-selective.sh"
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  tts_claude_md_template: "examples/claude-md/tts-enabled.md"
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- # Sandbox Isolation for Coding Agents (guide/sandbox-isolation.md) - Added 2026-01-31
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- sandbox_isolation_guide: "guide/sandbox-isolation.md"
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- sandbox_isolation_decision_tree: "guide/sandbox-isolation.md:7"
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- sandbox_docker_sandboxes: "guide/sandbox-isolation.md:67"
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- sandbox_docker_network: "guide/sandbox-isolation.md:121"
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- sandbox_docker_templates: "guide/sandbox-isolation.md:165"
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+ # Sandbox Isolation for Coding Agents (guide/security/sandbox-isolation.md) - Added 2026-01-31
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+ sandbox_isolation_guide: "guide/security/sandbox-isolation.md"
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+ sandbox_isolation_decision_tree: "guide/security/sandbox-isolation.md:7"
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+ sandbox_docker_sandboxes: "guide/security/sandbox-isolation.md:67"
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+ sandbox_docker_network: "guide/security/sandbox-isolation.md:121"
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+ sandbox_docker_templates: "guide/security/sandbox-isolation.md:165"
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  sandbox_docker_docs: "https://docs.docker.com/ai/sandboxes/"
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  sandbox_docker_claude_config: "https://docs.docker.com/ai/sandboxes/claude-code/"
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  sandbox_docker_network_docs: "https://docs.docker.com/ai/sandboxes/network-policies/"
@@ -204,26 +204,26 @@ deep_dive:
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  sandbox_cloudflare_sdk: "https://developers.cloudflare.com/sandbox/tutorials/claude-code/"
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  sandbox_vercel: "https://vercel.com/docs/vercel-sandbox/"
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  sandbox_e2b: "https://e2b.dev"
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- sandbox_native_cc: "guide/architecture.md:606"
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+ sandbox_native_cc: "guide/core/architecture.md:606"
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  # Native Claude Code Sandbox (Official docs, v2.1.0+) - Added 2026-02-02
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- sandbox_native_guide: "guide/sandbox-native.md"
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- sandbox_native_why: "guide/sandbox-native.md:47" # Why Native Sandboxing
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- sandbox_native_os_primitives: "guide/sandbox-native.md:68" # Seatbelt vs bubblewrap
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- sandbox_native_filesystem: "guide/sandbox-native.md:178" # Filesystem isolation
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- sandbox_native_network: "guide/sandbox-native.md:221" # Network proxy architecture
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- sandbox_native_modes: "guide/sandbox-native.md:7" # Auto-allow vs Regular
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- sandbox_native_escape_hatch: "guide/sandbox-native.md:341" # dangerouslyDisableSandbox
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- sandbox_native_security_limits: "guide/sandbox-native.md:396" # Domain fronting, Unix sockets
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- sandbox_native_opensource: "guide/sandbox-native.md:481" # Open-source runtime
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- sandbox_native_platforms: "guide/sandbox-native.md:505" # Platform support
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- sandbox_native_decision_tree: "guide/sandbox-native.md:517" # Native vs Docker
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- sandbox_native_config_examples: "guide/sandbox-native.md:564" # Configuration examples
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- sandbox_native_best_practices: "guide/sandbox-native.md:637" # Best practices
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- sandbox_native_troubleshooting: "guide/sandbox-native.md:650" # Troubleshooting
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+ sandbox_native_guide: "guide/security/sandbox-native.md"
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+ sandbox_native_why: "guide/security/sandbox-native.md:47" # Why Native Sandboxing
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+ sandbox_native_os_primitives: "guide/security/sandbox-native.md:68" # Seatbelt vs bubblewrap
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+ sandbox_native_filesystem: "guide/security/sandbox-native.md:178" # Filesystem isolation
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+ sandbox_native_network: "guide/security/sandbox-native.md:221" # Network proxy architecture
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+ sandbox_native_modes: "guide/security/sandbox-native.md:7" # Auto-allow vs Regular
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+ sandbox_native_escape_hatch: "guide/security/sandbox-native.md:341" # dangerouslyDisableSandbox
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+ sandbox_native_security_limits: "guide/security/sandbox-native.md:396" # Domain fronting, Unix sockets
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+ sandbox_native_opensource: "guide/security/sandbox-native.md:481" # Open-source runtime
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+ sandbox_native_platforms: "guide/security/sandbox-native.md:505" # Platform support
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+ sandbox_native_decision_tree: "guide/security/sandbox-native.md:517" # Native vs Docker
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+ sandbox_native_config_examples: "guide/security/sandbox-native.md:564" # Configuration examples
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+ sandbox_native_best_practices: "guide/security/sandbox-native.md:637" # Best practices
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+ sandbox_native_troubleshooting: "guide/security/sandbox-native.md:650" # Troubleshooting
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  sandbox_runtime_oss: "https://github.com/anthropic-experimental/sandbox-runtime"
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  sandbox_runtime_npm: "https://www.npmjs.com/package/@anthropic-ai/sandbox-runtime"
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  sandbox_official_docs: "https://code.claude.com/docs/en/sandboxing"
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- sandbox_comparison_native_docker: "guide/sandbox-isolation.md:238" # Section 4 Native CC
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+ sandbox_comparison_native_docker: "guide/security/sandbox-isolation.md:238" # Section 4 Native CC
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  sandbox_native_evaluation: "docs/resource-evaluations/native-sandbox-official-docs.md"
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  sandbox_native_score: "5/5"
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  # Templates (Added 2026-02-02)
@@ -232,19 +232,19 @@ deep_dive:
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  sandbox_validation_hook: "examples/hooks/bash/sandbox-validation.sh"
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  # Docker Sandboxes (existing)
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  sandbox_evaluation: "docs/resource-evaluations/docker-sandboxes-isolation.md"
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- sandbox_safe_autonomy: "guide/sandbox-isolation.md:496" # Safe Autonomy Workflows
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- sandbox_anti_patterns: "guide/sandbox-isolation.md:546" # Anti-Patterns
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- sandbox_comparison_matrix: "guide/sandbox-isolation.md:477" # Comparison Matrix
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+ sandbox_safe_autonomy: "guide/security/sandbox-isolation.md:496" # Safe Autonomy Workflows
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+ sandbox_anti_patterns: "guide/security/sandbox-isolation.md:546" # Anti-Patterns
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+ sandbox_comparison_matrix: "guide/security/sandbox-isolation.md:477" # Comparison Matrix
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  sandbox_score: "4/5"
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- # Third-Party Tools (guide/third-party-tools.md) - Added 2026-02-01
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- third_party_tools_guide: "guide/third-party-tools.md"
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- third_party_tools_cost_tracking: "guide/third-party-tools.md:42"
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- third_party_tools_rtk: "guide/third-party-tools.md:7"
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- third_party_tools_session_mgmt: "guide/third-party-tools.md:126"
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- third_party_tools_config_mgmt: "guide/third-party-tools.md:214"
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- third_party_tools_alternative_uis: "guide/third-party-tools.md:259"
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- third_party_tools_known_gaps: "guide/third-party-tools.md:375"
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- third_party_tools_recommendations: "guide/third-party-tools.md:391"
239
+ # Third-Party Tools (guide/ecosystem/third-party-tools.md) - Added 2026-02-01
240
+ third_party_tools_guide: "guide/ecosystem/third-party-tools.md"
241
+ third_party_tools_cost_tracking: "guide/ecosystem/third-party-tools.md:42"
242
+ third_party_tools_rtk: "guide/ecosystem/third-party-tools.md:7"
243
+ third_party_tools_session_mgmt: "guide/ecosystem/third-party-tools.md:126"
244
+ third_party_tools_config_mgmt: "guide/ecosystem/third-party-tools.md:214"
245
+ third_party_tools_alternative_uis: "guide/ecosystem/third-party-tools.md:259"
246
+ third_party_tools_known_gaps: "guide/ecosystem/third-party-tools.md:375"
247
+ third_party_tools_recommendations: "guide/ecosystem/third-party-tools.md:391"
248
248
  third_party_ccusage: "https://www.npmjs.com/package/ccusage"
249
249
  third_party_ccusage_site: "https://ccusage.com"
250
250
  third_party_ccburn: "https://github.com/JuanjoFuchs/ccburn"
@@ -291,18 +291,18 @@ deep_dive:
291
291
  permissions_deny_known_limitation: "background indexing may expose via system reminders before checks — GitHub #4160"
292
292
  permissions_deny_defense_in_depth: "store secrets outside project dir for guaranteed protection"
293
293
  # Visual Reference (ASCII diagrams)
294
- visual_reference: "guide/visual-reference.md"
295
- # Architecture internals (guide/architecture.md)
296
- architecture_visual_overview: "guide/architecture.md:51"
294
+ visual_reference: "guide/core/visual-reference.md"
295
+ # Architecture internals (guide/core/architecture.md)
296
+ architecture_visual_overview: "guide/core/architecture.md:51"
297
297
  architecture_visual_source: "https://www.linkedin.com/posts/mohamed-ali-ben-salem-2b777b9a_en-ce-moment-je-vois-passer-des-posts-du-activity-7420592149110362112-eY5a"
298
- architecture_master_loop: "guide/architecture.md:82"
299
- architecture_tools: "guide/architecture.md:219"
300
- architecture_context: "guide/architecture.md:312"
301
- architecture_subagents: "guide/architecture.md:471"
302
- architecture_permissions: "guide/architecture.md:541"
303
- architecture_mcp: "guide/architecture.md:746"
298
+ architecture_master_loop: "guide/core/architecture.md:82"
299
+ architecture_tools: "guide/core/architecture.md:219"
300
+ architecture_context: "guide/core/architecture.md:312"
301
+ architecture_subagents: "guide/core/architecture.md:471"
302
+ architecture_permissions: "guide/core/architecture.md:541"
303
+ architecture_mcp: "guide/core/architecture.md:746"
304
304
  architecture_mcp_visual: "guide/images/mcp-architecture-diagram.svg"
305
- architecture_philosophy: "guide/architecture.md:1205"
305
+ architecture_philosophy: "guide/core/architecture.md:1205"
306
306
  # Official LLM-Optimized Documentation - Added 2026-02-25
307
307
  official_llms_index: "https://code.claude.com/docs/llms.txt" # Index ~65 pages, ~15-20K tokens — use first for discovery
308
308
  official_llms_full: "https://code.claude.com/docs/llms-full.txt" # Full doc ~98KB, ~25-30K tokens — source de vérité officielle
@@ -310,9 +310,9 @@ deep_dive:
310
310
  system_prompts_official: "https://platform.claude.com/docs/en/release-notes/system-prompts"
311
311
  system_prompts_willison_analysis: "https://simonwillison.net/2025/May/25/claude-4-system-prompt/"
312
312
  system_prompts_prompthub: "https://www.prompthub.us/blog/an-analysis-of-the-claude-4-system-prompt"
313
- system_prompts_architecture: "guide/architecture.md:360"
313
+ system_prompts_architecture: "guide/core/architecture.md:360"
314
314
  # MCP Apps Extension (SEP-1865) - Added 2026-01-27
315
- mcp_apps_architecture: "guide/architecture.md:753"
315
+ mcp_apps_architecture: "guide/core/architecture.md:753"
316
316
  mcp_apps_evolution: "guide/ultimate-guide.md:9252"
317
317
  mcp_apps_spec: "https://github.com/modelcontextprotocol/ext-apps"
318
318
  mcp_apps_blog_mcp: "https://blog.modelcontextprotocol.io/posts/2026-01-26-mcp-apps/"
@@ -534,16 +534,16 @@ deep_dive:
534
534
  - "Linear MCP: ~9.5k installs (issue tracking)"
535
535
  plugins_awesome_list: "https://github.com/hesreallyhim/awesome-claude-code"
536
536
  plugins_awesome_list_stars: "20k+"
537
- chain_of_verification: "guide/methodologies.md:230"
537
+ chain_of_verification: "guide/core/methodologies.md:230"
538
538
  chain_of_verification_paper: "https://arxiv.org/abs/2309.11495"
539
539
  chain_of_verification_acl: "https://aclanthology.org/2024.findings-acl.212/"
540
540
  # Verification Loops & Eval Harness (added 2026-01-23)
541
- verification_loops: "guide/methodologies.md:245"
541
+ verification_loops: "guide/core/methodologies.md:245"
542
542
  verification_loops_source: "https://www.anthropic.com/engineering/claude-code-best-practices"
543
- eval_harness: "guide/methodologies.md:289"
543
+ eval_harness: "guide/core/methodologies.md:289"
544
544
  eval_harness_source: "https://www.anthropic.com/engineering/demystifying-evals-for-ai-agents"
545
545
  # GSD (Get Shit Done) methodology (added 2026-01-25)
546
- gsd_methodology: "guide/methodologies.md:53"
546
+ gsd_methodology: "guide/core/methodologies.md:53"
547
547
  gsd_evaluation: "docs/resource-evaluations/gsd-evaluation.md"
548
548
  gsd_source: "https://github.com/glittercowboy/get-shit-done"
549
549
  gsd_note: "Overlap with existing patterns (Ralph Loop, Gas Town, BMAD)"
@@ -572,35 +572,35 @@ deep_dive:
572
572
  audit_agents_skills_industry_context: "29.5% deploy without evaluation (LangChain 2026), 18% cite agent bugs as top challenge"
573
573
  audit_agents_skills_guide_refs: "guide/ultimate-guide.md:4951 (after Agent Validation Checklist), guide/ultimate-guide.md:5495 (after Skill Validation)"
574
574
  # Practitioner Insights (external validation)
575
- practitioner_insights: "guide/ai-ecosystem.md:2170"
576
- practitioner_dave_van_veen: "guide/ai-ecosystem.md:2174"
577
- practitioner_matteo_collina: "guide/ai-ecosystem.md:2203"
575
+ practitioner_insights: "guide/ecosystem/ai-ecosystem.md:2170"
576
+ practitioner_dave_van_veen: "guide/ecosystem/ai-ecosystem.md:2174"
577
+ practitioner_matteo_collina: "guide/ecosystem/ai-ecosystem.md:2203"
578
578
  # Outcome Engineering (o16g) - Emerging manifesto (2026-02-13)
579
- outcome_engineering_o16g: "guide/ai-ecosystem.md:2366"
579
+ outcome_engineering_o16g: "guide/ecosystem/ai-ecosystem.md:2366"
580
580
  outcome_engineering_url: "https://o16g.com/"
581
581
  outcome_engineering_author: "Cory Ondrejka (CTO Onebrief, co-creator Second Life, ex-VP Google/Meta)"
582
582
  outcome_engineering_status: "Emerging - on watch list for community adoption"
583
583
  practitioner_collina_source: "https://adventures.nodeland.dev/archive/the-human-in-the-loop/"
584
- practitioner_steinberger: "guide/ai-ecosystem.md:2242"
584
+ practitioner_steinberger: "guide/ecosystem/ai-ecosystem.md:2242"
585
585
  practitioner_steinberger_source: "https://steipete.me/posts/2025/shipping-at-inference-speed"
586
- practitioner_addy_osmani: "guide/ai-ecosystem.md:2269"
586
+ practitioner_addy_osmani: "guide/ecosystem/ai-ecosystem.md:2269"
587
587
  practitioner_osmani_source: "https://addyo.substack.com/p/the-80-problem-in-agentic-coding"
588
- practitioner_alan: "guide/ai-ecosystem.md:2299"
588
+ practitioner_alan: "guide/ecosystem/ai-ecosystem.md:2299"
589
589
  practitioner_alan_source: "https://www.linkedin.com/pulse/le-principe-de-la-tour-eiffel-et-ralph-wiggum-maxime-le-bras-psmxe/"
590
- verification_paradox: "guide/production-safety.md:639"
590
+ verification_paradox: "guide/security/production-safety.md:639"
591
591
  verification_paradox_source: "https://www.linkedin.com/pulse/le-principe-de-la-tour-eiffel-et-ralph-wiggum-maxime-le-bras-psmxe/"
592
- eighty_percent_problem: "guide/ai-ecosystem.md:2269"
593
- comprehension_debt_secondary: "guide/ai-ecosystem.md:2269" # See also: vibe_coding_trap (primary)
594
- # DevOps/SRE Guide (guide/devops-sre.md)
595
- devops_sre_guide: "guide/devops-sre.md"
596
- devops_fire_framework: "guide/devops-sre.md:46"
597
- devops_k8s_troubleshooting: "guide/devops-sre.md:129"
598
- devops_k8s_prompts: "guide/devops-sre.md:151"
599
- devops_incident_response: "guide/devops-sre.md:333"
600
- devops_iac_patterns: "guide/devops-sre.md:504"
601
- devops_guardrails: "guide/devops-sre.md:687"
602
- devops_limitations: "guide/devops-sre.md:297"
603
- devops_quick_reference: "guide/devops-sre.md:794"
592
+ eighty_percent_problem: "guide/ecosystem/ai-ecosystem.md:2269"
593
+ comprehension_debt_secondary: "guide/ecosystem/ai-ecosystem.md:2269" # See also: vibe_coding_trap (primary)
594
+ # DevOps/SRE Guide (guide/ops/devops-sre.md)
595
+ devops_sre_guide: "guide/ops/devops-sre.md"
596
+ devops_fire_framework: "guide/ops/devops-sre.md:46"
597
+ devops_k8s_troubleshooting: "guide/ops/devops-sre.md:129"
598
+ devops_k8s_prompts: "guide/ops/devops-sre.md:151"
599
+ devops_incident_response: "guide/ops/devops-sre.md:333"
600
+ devops_iac_patterns: "guide/ops/devops-sre.md:504"
601
+ devops_guardrails: "guide/ops/devops-sre.md:687"
602
+ devops_limitations: "guide/ops/devops-sre.md:297"
603
+ devops_quick_reference: "guide/ops/devops-sre.md:794"
604
604
  devops_agent: "examples/agents/devops-sre.md"
605
605
  devops_claude_md: "examples/claude-md/devops-sre.md"
606
606
  # Product Designer (design-to-code workflow)
@@ -691,19 +691,19 @@ deep_dive:
691
691
  author: "Steve Yegge"
692
692
  description: "Multi-agent workspace manager using Claude Code instances"
693
693
  status: "Experimental (Jan 2026)"
694
- guide_section: "guide/ai-ecosystem.md:850"
694
+ guide_section: "guide/ecosystem/ai-ecosystem.md:850"
695
695
  multiclaude:
696
696
  repo: "https://github.com/dlorenc/multiclaude"
697
697
  author: "dlorenc"
698
698
  description: "Self-hosted multi-agent Claude Code spawner (tmux + git worktrees)"
699
699
  status: "Active development (Jan 2026, 383 stars)"
700
- guide_section: "guide/ai-ecosystem.md:850"
700
+ guide_section: "guide/ecosystem/ai-ecosystem.md:850"
701
701
  agent_chat:
702
702
  repo: "https://github.com/justinabrahms/agent-chat"
703
703
  author: "Justin Abrahms"
704
704
  description: "Real-time monitoring UI for Gas Town and multiclaude (SSE + SQLite)"
705
705
  status: "Early preview (Jan 2026, v0.2.0)"
706
- guide_section: "guide/ai-ecosystem.md:850"
706
+ guide_section: "guide/ecosystem/ai-ecosystem.md:850"
707
707
  # External research & alignment tools
708
708
  external_research:
709
709
  claude_constitution:
@@ -713,7 +713,7 @@ deep_dive:
713
713
  description: "Claude's Constitutional AI framework - value hierarchy (safety > ethics > compliance > utility)"
714
714
  license: "CC0 1.0 (public domain)"
715
715
  published: "2026-01-21"
716
- guide_section: "guide/data-privacy.md:296"
716
+ guide_section: "guide/security/data-privacy.md:296"
717
717
  petri_v2:
718
718
  repo: "https://github.com/safety-research/petri"
719
719
  blog: "https://alignment.anthropic.com/2026/petri-v2/"
@@ -830,7 +830,7 @@ deep_dive:
830
830
  spec_osmani_score: "4/5"
831
831
  spec_task_granularity: "guide/workflows/spec-first.md:62" # Vertical slices + PRD checklist (Allan Hill, Feb 2026)
832
832
  spec_prd_checklist: "guide/workflows/spec-first.md:68" # 6-dimension PRD quality checklist
833
- atdd_with_agents: "guide/methodologies.md:161" # ATDD + Gherkin for agentic workflows
833
+ atdd_with_agents: "guide/core/methodologies.md:161" # ATDD + Gherkin for agentic workflows
834
834
  commands_table: 47
835
835
  shortcuts_table: 368
836
836
  troubleshooting: 11311
@@ -842,23 +842,23 @@ deep_dive:
842
842
  ai_ecosystem_tool_matrix: 20031
843
843
  ai_ecosystem_workflows: 20166
844
844
  ai_ecosystem_integration: 20294
845
- ai_ecosystem_detailed: "guide/ai-ecosystem.md"
846
- ai_ecosystem_goose: "guide/ai-ecosystem.md:2074"
847
- ai_ecosystem_goose_comparison: "guide/ai-ecosystem.md:2090"
848
- ai_ecosystem_context_packing: "guide/ai-ecosystem.md:2533"
849
- ai_ecosystem_multi_ide_sync: "guide/ai-ecosystem.md:1282"
850
- agents_md_support_status: "guide/ai-ecosystem.md:1348"
851
- ai_ecosystem_build_vs_use: "guide/ai-ecosystem.md:2399" # Section 11.3 - When to Build vs Use (ADK, LangChain, Vercel AI SDK)
845
+ ai_ecosystem_detailed: "guide/ecosystem/ai-ecosystem.md"
846
+ ai_ecosystem_goose: "guide/ecosystem/ai-ecosystem.md:2074"
847
+ ai_ecosystem_goose_comparison: "guide/ecosystem/ai-ecosystem.md:2090"
848
+ ai_ecosystem_context_packing: "guide/ecosystem/ai-ecosystem.md:2533"
849
+ ai_ecosystem_multi_ide_sync: "guide/ecosystem/ai-ecosystem.md:1282"
850
+ agents_md_support_status: "guide/ecosystem/ai-ecosystem.md:1348"
851
+ ai_ecosystem_build_vs_use: "guide/ecosystem/ai-ecosystem.md:2399" # Section 11.3 - When to Build vs Use (ADK, LangChain, Vercel AI SDK)
852
852
  # Architecture Diagrams as Context (advanced pattern) - Added 2026-01-25
853
- architecture_diagrams_input: "guide/ai-ecosystem.md:2567"
853
+ architecture_diagrams_input: "guide/ecosystem/ai-ecosystem.md:2567"
854
854
  architecture_diagrams_mcp_tools:
855
855
  - "Archy MCP: https://www.pulsemcp.com/servers/phxdev1-archy"
856
856
  - "Mermaid MCP: 61.4K users"
857
857
  - "Blueprint MCP (ArcadeAI)"
858
858
  llm_oop_research: "https://dl.acm.org/doi/10.1145/3639474.3640052"
859
859
  architecture_diagrams_source: "https://www.linkedin.com/posts/tigraff_uml-claude-wibecoding-activity-7420595633826258944-gGO5"
860
- ai_ecosystem_voice_to_text: "guide/ai-ecosystem.md:1066"
861
- ai_ecosystem_alternative_providers: "guide/ai-ecosystem.md:2639"
860
+ ai_ecosystem_voice_to_text: "guide/ecosystem/ai-ecosystem.md:1066"
861
+ ai_ecosystem_alternative_providers: "guide/ecosystem/ai-ecosystem.md:2639"
862
862
  voice_refine_skill: "examples/skills/voice-refine/SKILL.md"
863
863
  # Cowork documentation (v1.0 - migrated to dedicated repo)
864
864
  cowork_reference: "machine-readable/cowork-reference.yaml" # Dedicated YAML index (kept local)
@@ -874,7 +874,7 @@ deep_dive:
874
874
  cowork_faq: "https://github.com/FlorianBruniaux/claude-cowork-guide/blob/main/reference/faq.md"
875
875
  cowork_prompts: "https://github.com/FlorianBruniaux/claude-cowork-guide/tree/main/prompts"
876
876
  cowork_workflows: "https://github.com/FlorianBruniaux/claude-cowork-guide/tree/main/workflows"
877
- cowork_section: "guide/ai-ecosystem.md:1809"
877
+ cowork_section: "guide/ecosystem/ai-ecosystem.md:1809"
878
878
  cowork_ultimate_guide: 20348
879
879
  # Experimental Features
880
880
  teammatetool: 3976
@@ -914,25 +914,25 @@ deep_dive:
914
914
  workflow: 58 # Workflow (9 steps)
915
915
  fix: 11948 # Troubleshooting section
916
916
  architecture: 919 # Architecture internals
917
- production_safety: "guide/production-safety.md" # Production safety rules
918
- security_hardening: "guide/security-hardening.md" # Security best practices
919
- security_cve_summary: "guide/security-hardening.md:15" # Decision Matrix + CVEs
920
- security_supply_chain_stats: "guide/security-hardening.md:137" # Agent Skills Supply Chain Risks
921
- security_mcp_scan_tool: "guide/security-hardening.md:32" # MCP Vetting Workflow
922
- security_malicious_extensions: "guide/security-hardening.md:252" # .claude/ attack surface (§1.5)
923
- security_kill_switch: "guide/security-hardening.md:630" # AI Kill Switch & Containment Architecture (§3.5)
924
- security_claude_folder_audit: "guide/security-hardening.md:228" # Repository Pre-Scan (§1.4)
917
+ production_safety: "guide/security/production-safety.md" # Production safety rules
918
+ security_hardening: "guide/security/security-hardening.md" # Security best practices
919
+ security_cve_summary: "guide/security/security-hardening.md:15" # Decision Matrix + CVEs
920
+ security_supply_chain_stats: "guide/security/security-hardening.md:137" # Agent Skills Supply Chain Risks
921
+ security_mcp_scan_tool: "guide/security/security-hardening.md:32" # MCP Vetting Workflow
922
+ security_malicious_extensions: "guide/security/security-hardening.md:252" # .claude/ attack surface (§1.5)
923
+ security_kill_switch: "guide/security/security-hardening.md:630" # AI Kill Switch & Containment Architecture (§3.5)
924
+ security_claude_folder_audit: "guide/security/security-hardening.md:228" # Repository Pre-Scan (§1.4)
925
925
  security_toxicskills_evaluation: "docs/resource-evaluations/snyk-toxicskills-evaluation.md"
926
926
  security_check_command: "examples/commands/security-check.md" # Quick config check vs known threats
927
927
  security_audit_command: "examples/commands/security-audit.md" # Full 6-phase security audit (score /100)
928
928
  security_threat_db: "examples/commands/resources/threat-db.yaml" # Threat intelligence database (authors, skills, CVEs, patterns)
929
929
  security_update_threat_db: "examples/commands/update-threat-db.md" # /update-threat-db — research & update threat database
930
- security_cc_scanner: "guide/security-hardening.md:780" # Claude Code Security (research preview) — Anthropic native vuln scanner, adversarial validation, patch suggestions
930
+ security_cc_scanner: "guide/security/security-hardening.md:780" # Claude Code Security (research preview) — Anthropic native vuln scanner, adversarial validation, patch suggestions
931
931
  security_patcher_agent: "examples/agents/security-patcher.md" # Agent: applies patches from security-auditor findings, human approval gate, Write/Edit tools
932
932
  security_gate_hook: "examples/hooks/bash/security-gate.sh" # PreToolUse hook: blocks 7 vuln patterns at write time (SQLi, XSS, hardcoded secrets, eval, weak hash, cmd injection, path traversal)
933
- security_pr_review_workflow: "guide/security-hardening.md:712" # PR security review workflow — 3-agent pipeline, git hook integration
933
+ security_pr_review_workflow: "guide/security/security-hardening.md:712" # PR security review workflow — 3-agent pipeline, git hook integration
934
934
  agent_validation_checklist: 5744 # Agent validation section in ultimate-guide.md
935
- git_mcp_guide: "guide/mcp-servers-ecosystem.md:113" # Git MCP server documentation
935
+ git_mcp_guide: "guide/ecosystem/mcp-servers-ecosystem.md:113" # Git MCP server documentation
936
936
 
937
937
  # ════════════════════════════════════════════════════════════════
938
938
  # DECISION TREE (most important - en premier)
@@ -1102,10 +1102,10 @@ mcp:
1102
1102
  playwright: "browser automation / E2E"
1103
1103
  figma: "design file access, tokens, structure (official)"
1104
1104
  git_mcp: "version control automation (official Anthropic) - 12 tools for commits, branches, diffs, logs"
1105
- git_mcp_guide: "guide/mcp-servers-ecosystem.md:102"
1105
+ git_mcp_guide: "guide/ecosystem/mcp-servers-ecosystem.md:102"
1106
1106
  git_mcp_tools: "git_status, git_log, git_diff, git_commit, git_add, git_reset, git_branch, git_create_branch, git_checkout, git_show, git_diff_unstaged, git_diff_staged"
1107
1107
  git_mcp_install: "uvx mcp-server-git --repository /path/to/repo"
1108
- git_mcp_decision_matrix: "guide/mcp-servers-ecosystem.md:212" # Git MCP vs GitHub MCP vs Bash tool
1108
+ git_mcp_decision_matrix: "guide/ecosystem/mcp-servers-ecosystem.md:212" # Git MCP vs GitHub MCP vs Bash tool
1109
1109
  git_mcp_repo: "https://github.com/modelcontextprotocol/servers/tree/main/src/git"
1110
1110
  git_mcp_score: "8.5/10"
1111
1111
  git_mcp_status: "Early development (API subject to change)"
@@ -1120,7 +1120,7 @@ mcp:
1120
1120
  search_decision_tree: "grep (text) | ast-grep (structure) | Serena (symbols) | grepai (semantic)"
1121
1121
  search_tools_comparison: "guide/ultimate-guide.md:9845"
1122
1122
  search_tools_mastery_workflow: "guide/workflows/search-tools-mastery.md"
1123
- grep_vs_rag_history: "guide/architecture.md:232"
1123
+ grep_vs_rag_history: "guide/core/architecture.md:232"
1124
1124
  ripgrep_native: "Grep tool (Claude Code built-in, ~20ms)"
1125
1125
  grepai_semantic: "Semantic search + call graph (Ollama-based, ~500ms)"
1126
1126
  grepai_benchmark:
@@ -1136,10 +1136,10 @@ mcp:
1136
1136
  config: "~/.claude.json (mcpServers field) or .mcp.json (project root)"
1137
1137
  tool_search: "lazy loading MCP tools (v2.1.7+) - 85% token reduction - auto:N threshold config"
1138
1138
  tool_search_config: "ENABLE_TOOL_SEARCH=auto|auto:N|true|false"
1139
- tool_search_deep_dive: "guide/architecture.md:284"
1139
+ tool_search_deep_dive: "guide/core/architecture.md:284"
1140
1140
 
1141
1141
  # ════════════════════════════════════════════════════════════════
1142
- # ARCHITECTURE INTERNALS - see guide/architecture.md
1142
+ # ARCHITECTURE INTERNALS - see guide/core/architecture.md
1143
1143
  # ════════════════════════════════════════════════════════════════
1144
1144
  architecture:
1145
1145
  master_loop: "while(tool_call) - no DAG, no classifier, no RAG"
@@ -1150,7 +1150,7 @@ architecture:
1150
1150
  philosophy: "less scaffolding, more model - trust Claude's reasoning"
1151
1151
  mcp_protocol: "JSON-RPC 2.0, treated as native tools"
1152
1152
  permissions: "interactive prompts + allow/deny rules + hooks"
1153
- deep_dive: "guide/architecture.md"
1153
+ deep_dive: "guide/core/architecture.md"
1154
1154
 
1155
1155
  # ════════════════════════════════════════════════════════════════
1156
1156
  # COST OPTIMIZATION - see deep_dive.cost_optimization
@@ -1346,7 +1346,7 @@ ecosystem:
1346
1346
  focus: "Production-grade agentic coding guardrails (TDD, worktrees, manual commits)"
1347
1347
  academic: "Co-author 'Agentic Systems in Radiology' (ArXiv 2025)"
1348
1348
  alignment: "Validates patterns already documented in this guide"
1349
- guide_section: "guide/ai-ecosystem.md:1209"
1349
+ guide_section: "guide/ecosystem/ai-ecosystem.md:1209"
1350
1350
  install_templates: "scripts/install-templates.sh"
1351
1351
  cowork:
1352
1352
  description: "Claude Code for non-developers (desktop app)"