fix(docs): critical factual corrections v3.6.1

Major audit correcting misleading documentation about Claude Code behavior:

### Fixed
- `--add-dir`: permissions (not context loading)
- `excludePatterns` → `permissions.deny` (never existed)
- `.claudeignore` removed (not an official feature)
- "selective loading" myth → lazy loading reality
- Invented CLI flags (`--think`, `--headless`, `--learn`) → prompt keywords
- `@` file reference: "loads automatically" → "reads on-demand"

### Added
- Session Search Tool (`cs`) - zero-dep bash script for finding sessions
- Security section: Known limitations of permissions.deny

15 files modified, 516 insertions, 200 deletions

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

machine-readable/reference.yaml

@@ -3,7 +3,7 @@
 # Source: guide/ultimate-guide.md
 # Purpose: Condensed index for LLMs to quickly answer user questions about Claude Code
 
-version: "3.6.0"
+version: "3.6.1"
 updated: "2026-01"
 
 # ════════════════════════════════════════════════════════════════
@@ -12,6 +12,9 @@ updated: "2026-01"
 # For architecture internals, see guide/architecture.md
 # ════════════════════════════════════════════════════════════════
 deep_dive:
+  # Session management
+  session_search: "guide/observability.md:29"
+  session_search_script: "examples/scripts/session-search.sh"
   # Architecture internals (guide/architecture.md)
   architecture_master_loop: "guide/architecture.md:60"
   architecture_tools: "guide/architecture.md:130"
@@ -53,7 +56,6 @@ deep_dive:
   mcp_servers: 4573
   mcp_config: 4771
   mcp_security: 5373
-  trinity_pattern: 5171
   cicd: 5329
   ide_integration: 6018
   feedback_loops: 6088
@@ -78,8 +80,7 @@ decide:
   context_high: "/compact (>70%) or /clear (>90%)"
   repeating: "create agent or command"
   need_docs: "Context7 MCP"
-  deep_debug: "--think or --ultrathink"
-  learning: "--learn (want to understand decisions)"
+  deep_debug: "use extended thinking in prompts"
 
 # ════════════════════════════════════════════════════════════════
 # PROMPTING FORMULA (see deep_dive.xml_prompting for details)
@@ -141,14 +142,10 @@ cli:
   "-c": "continue last session"
   "-r <id>": "resume specific session"
   "-p": "non-interactive (pipe mode)"
-  "--headless": "CI/CD mode"
   "--model X": "select model"
   "--dangerously-skip-permissions": "auto-accept ALL (danger)"
   "--debug": "verbose output"
-  "--mcp-debug": "debug MCP servers"
-  "--learn": "enable learning mode (explanations)"
-  "--learn focus:X": "learn only for domain (git/arch/sec)"
-  "--no-learn": "suppress learning offers"
+  "--add-dir": "grant tool access to directories outside CWD"
 
 # ════════════════════════════════════════════════════════════════
 # CONTEXT MANAGEMENT - see deep_dive.context_management
@@ -220,14 +217,6 @@ architecture:
   permissions: "interactive prompts + allow/deny rules + hooks"
   deep_dive: "guide/architecture.md"
 
-# ════════════════════════════════════════════════════════════════
-# THINK LEVELS - see deep_dive.trinity_pattern
-# ════════════════════════════════════════════════════════════════
-think:
-  "--think": "~4K tokens - moderate analysis"
-  "--think-hard": "~10K tokens - architecture"
-  "--ultrathink": "~32K tokens - critical redesign"
-
 # ════════════════════════════════════════════════════════════════
 # COST OPTIMIZATION - see deep_dive.cost_optimization
 # ════════════════════════════════════════════════════════════════
@@ -236,7 +225,7 @@ cost:
   sonnet: "most development ($$)"
   opus: "architecture, complex bugs ($$$)"
   opusplan: "plan=opus + execute=sonnet ($$)"
-  tip: "use --add-dir to limit loaded dirs"
+  tip: "--add-dir grants tool access to additional directories (permissions, not context loading)"
 
 # ════════════════════════════════════════════════════════════════
 # TOOL SELECTION
@@ -259,7 +248,7 @@ dont:
   - "accept without reading → read every diff"
   - "ignore >70% context → /compact"
   - "skip permissions in prod → never"
-  - "load giant context → load only needed"
+  - "bloated CLAUDE.md → keep concise (<200 lines)"
   - "only negative constraints → provide alternatives"
 
 # ════════════════════════════════════════════════════════════════
@@ -330,7 +319,7 @@ onboarding_matrix:
   optimize:
     intermediate_15min: [context_management, context_triage, plan_mode]
     intermediate_30min: [context_management, plan_mode, memory_files, cost_optimization]
-    power_30min: [context_triage, trinity_pattern, batch_operations]
+    power_30min: [context_triage, cost_optimization, batch_operations]
 
   build_agents:
     intermediate_30min: [agents, agent_template, agent_examples]
@@ -343,7 +332,7 @@ onboarding_matrix:
   learn_everything:
     beginner_60min: [workflow, essential_commands, context_management, memory_files, plan_mode]
     intermediate_120min: [plan_mode, agents, skills, hooks, mcp_servers]
-    power_120min: [architecture, mcp_servers, hooks, trinity_pattern, cicd]
+    power_120min: [architecture, mcp_servers, hooks, cost_optimization, cicd]
 
 # ════════════════════════════════════════════════════════════════
 # ONBOARDING QUESTIONS - Structure for interactive profiling