deepthinking-mcp 2.0.0 → 2.1.0

package/README.md

@@ -1,10 +1,10 @@
-# DeepThinking MCP v2.0
+# DeepThinking MCP v2.1
 
-A comprehensive Model Context Protocol (MCP) server featuring **10 advanced reasoning modes** for complex problem-solving, analysis, and decision-making.
+A comprehensive Model Context Protocol (MCP) server featuring **11 advanced reasoning modes** for complex problem-solving, analysis, and decision-making.
 
 ## Overview
 
-DeepThinking MCP v2.0 provides a complete toolkit for structured reasoning with 10 specialized modes:
+DeepThinking MCP v2.1 provides a complete toolkit for structured reasoning with 11 specialized modes:
 
 ### Core Modes
 - **Sequential**: Iterative refinement with revision capabilities
@@ -19,10 +19,12 @@ DeepThinking MCP v2.0 provides a complete toolkit for structured reasoning with
 - **Bayesian**: Probabilistic reasoning with evidence updates
 - **Counterfactual**: What-if scenario analysis and alternative histories
 - **Analogical**: Cross-domain pattern matching and knowledge transfer
+n### Phase 3 Modes (v2.1+)
+- **Temporal**: Event timelines, temporal constraints, Allen's interval algebra, causal relations over time
 
 ## Features
 
-### 10 Specialized Reasoning Modes
+### 11 Specialized Reasoning Modes
 
 #### Core Modes
 - **Sequential**: Iterative refinement with revision capabilities and branching
@@ -37,6 +39,8 @@ DeepThinking MCP v2.0 provides a complete toolkit for structured reasoning with
 - **Bayesian**: Update beliefs using probabilistic reasoning with priors, likelihoods, and evidence. Essential for risk assessment and A/B testing.
 - **Counterfactual**: Explore alternative scenarios and compare outcomes. Excellent for post-mortems and strategic planning.
 - **Analogical**: Transfer knowledge across domains by identifying structural similarities. Great for design patterns and innovative problem-solving.
+n#### Phase 3 Reasoning Modes (v2.1+)
+- **Temporal**: Model events, intervals, and temporal relationships using Allen's interval algebra. Track causality over time with timestamps, durations, and temporal constraints. Perfect for timeline analysis, scheduling problems, and understanding event sequences.
 
 ### Mathematical Enhancements
 - **Symbolic computation** support with LaTeX and symbolic formats
@@ -116,7 +120,7 @@ The hybrid mode automatically selects the best features from each mode.
 - `thoughtNumber` (number, required): Position in sequence
 - `totalThoughts` (number, required): Estimated total thoughts needed
 - `nextThoughtNeeded` (boolean, required): Whether to continue thinking
-- `mode` (string, optional): `sequential`, `shannon`, `mathematics`, `physics`, `hybrid`, `abductive`, `causal`, `bayesian`, `counterfactual`, or `analogical` (default: `hybrid`)
+- `mode` (string, optional): `sequential`, `shannon`, `mathematics`, `physics`, `hybrid`, `abductive`, `causal`, `bayesian`, `counterfactual`, `analogical`, or `temporal` (default: `hybrid`)
 
 ### Mode-Specific Parameters
 
@@ -179,6 +183,12 @@ The hybrid mode automatically selects the best features from each mode.
 - `inferences`: Predictions based on analogical reasoning
 - `limitations`: Where the analogy breaks down
 - `analogyStrength`: Overall confidence in the analogy (0-1)
+n#### Temporal Mode
+- `timeline`: Timeline structure with id, name, timeUnit, events array
+- `events`: Temporal events (instant or interval) with timestamps, duration, properties
+- `intervals`: Time intervals with start, end, overlaps, contains relationships
+- `constraints`: Allen's interval algebra constraints (before, after, during, overlaps, meets, starts, finishes, equals)
+- `relations`: Temporal causal relations (causes, enables, prevents, precedes, follows) with strength and delay
 
 ### Actions
 - `add_thought` (default): Add a new thought to session

package/dist/index.js

@@ -7,7 +7,7 @@ import { z } from 'zod';
 
 var ThinkingToolSchema = z.object({
   sessionId: z.string().optional(),
-  mode: z.enum(["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical"]).default("hybrid"),
+  mode: z.enum(["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical", "temporal", "gametheory", "evidential"]).default("hybrid"),
   thought: z.string(),
   thoughtNumber: z.number().int().positive(),
   totalThoughts: z.number().int().positive(),
@@ -44,13 +44,54 @@ var ThinkingToolSchema = z.object({
     units: z.string(),
     conservationLaws: z.array(z.string())
   }).optional(),
+  // Temporal reasoning properties (Phase 3, v2.1)
+  timeline: z.object({
+    id: z.string(),
+    name: z.string(),
+    timeUnit: z.enum(["milliseconds", "seconds", "minutes", "hours", "days", "months", "years"]),
+    startTime: z.number().optional(),
+    endTime: z.number().optional(),
+    events: z.array(z.string())
+  }).optional(),
+  events: z.array(z.object({
+    id: z.string(),
+    name: z.string(),
+    description: z.string(),
+    timestamp: z.number(),
+    duration: z.number().optional(),
+    type: z.enum(["instant", "interval"]),
+    properties: z.record(z.any())
+  })).optional(),
+  intervals: z.array(z.object({
+    id: z.string(),
+    name: z.string(),
+    start: z.number(),
+    end: z.number(),
+    overlaps: z.array(z.string()).optional(),
+    contains: z.array(z.string()).optional()
+  })).optional(),
+  constraints: z.array(z.object({
+    id: z.string(),
+    type: z.enum(["before", "after", "during", "overlaps", "meets", "starts", "finishes", "equals"]),
+    subject: z.string(),
+    object: z.string(),
+    confidence: z.number().min(0).max(1)
+  })).optional(),
+  relations: z.array(z.object({
+    id: z.string(),
+    from: z.string(),
+    to: z.string(),
+    relationType: z.enum(["causes", "enables", "prevents", "precedes", "follows"]),
+    strength: z.number().min(0).max(1),
+    delay: z.number().optional()
+  })).optional(),
   action: z.enum(["add_thought", "summarize", "export", "switch_mode", "get_session"]).default("add_thought"),
   exportFormat: z.enum(["markdown", "latex", "json", "html", "jupyter"]).optional(),
-  newMode: z.enum(["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical"]).optional()
+  newMode: z.enum(["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical", "temporal", "gametheory", "evidential"]).optional()
 });
 var thinkingTool = {
   name: "deepthinking",
-  description: `Advanced deep thinking tool supporting 10 reasoning modes:
+  description: `Advanced deep thinking tool supporting 13 reasoning modes:
 
 Core Modes:
 - sequential: Iterative refinement and exploration
@@ -66,6 +107,11 @@ Advanced Modes (v2.0):
 - counterfactual: What-if scenario analysis
 - analogical: Cross-domain pattern matching and insights
 
+Phase 3 Modes (v2.1+):
+- temporal: Event timelines, temporal constraints, causal relations over time
+- gametheory: Nash equilibria, strategic analysis, payoff matrices
+- evidential: Dempster-Shafer theory, belief functions, evidence combination
+
 Choose the mode that best fits your problem type.`,
   inputSchema: {
     type: "object",
@@ -76,7 +122,7 @@ Choose the mode that best fits your problem type.`,
       },
       mode: {
         type: "string",
-        enum: ["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical"],
+        enum: ["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical", "temporal", "gametheory", "evidential"],
         description: "Thinking mode to use"
       },
       thought: {
@@ -203,6 +249,125 @@ Choose the mode that best fits your problem type.`,
         },
         required: ["quantity", "units", "conservationLaws"]
       },
+      // Temporal reasoning properties (Phase 3, v2.1)
+      timeline: {
+        type: "object",
+        properties: {
+          id: { type: "string" },
+          name: { type: "string" },
+          timeUnit: {
+            type: "string",
+            enum: ["milliseconds", "seconds", "minutes", "hours", "days", "months", "years"],
+            description: "Time unit for the timeline"
+          },
+          startTime: { type: "number", description: "Optional start time" },
+          endTime: { type: "number", description: "Optional end time" },
+          events: {
+            type: "array",
+            items: { type: "string" },
+            description: "Event IDs in this timeline"
+          }
+        },
+        required: ["id", "name", "timeUnit", "events"],
+        description: "Timeline structure for temporal reasoning"
+      },
+      events: {
+        type: "array",
+        items: {
+          type: "object",
+          properties: {
+            id: { type: "string" },
+            name: { type: "string" },
+            description: { type: "string" },
+            timestamp: { type: "number", description: "Event timestamp" },
+            duration: { type: "number", description: "Duration for interval events" },
+            type: {
+              type: "string",
+              enum: ["instant", "interval"],
+              description: "Event type"
+            },
+            properties: {
+              type: "object",
+              description: "Additional event properties"
+            }
+          },
+          required: ["id", "name", "description", "timestamp", "type", "properties"]
+        },
+        description: "Temporal events"
+      },
+      intervals: {
+        type: "array",
+        items: {
+          type: "object",
+          properties: {
+            id: { type: "string" },
+            name: { type: "string" },
+            start: { type: "number", description: "Interval start time" },
+            end: { type: "number", description: "Interval end time" },
+            overlaps: {
+              type: "array",
+              items: { type: "string" },
+              description: "IDs of overlapping intervals"
+            },
+            contains: {
+              type: "array",
+              items: { type: "string" },
+              description: "IDs of contained intervals"
+            }
+          },
+          required: ["id", "name", "start", "end"]
+        },
+        description: "Time intervals with Allen's algebra relationships"
+      },
+      constraints: {
+        type: "array",
+        items: {
+          type: "object",
+          properties: {
+            id: { type: "string" },
+            type: {
+              type: "string",
+              enum: ["before", "after", "during", "overlaps", "meets", "starts", "finishes", "equals"],
+              description: "Allen's interval algebra constraint type"
+            },
+            subject: { type: "string", description: "Subject event/interval ID" },
+            object: { type: "string", description: "Object event/interval ID" },
+            confidence: {
+              type: "number",
+              minimum: 0,
+              maximum: 1,
+              description: "Confidence in constraint (0-1)"
+            }
+          },
+          required: ["id", "type", "subject", "object", "confidence"]
+        },
+        description: "Temporal constraints using Allen's interval algebra"
+      },
+      relations: {
+        type: "array",
+        items: {
+          type: "object",
+          properties: {
+            id: { type: "string" },
+            from: { type: "string", description: "Source event ID" },
+            to: { type: "string", description: "Target event ID" },
+            relationType: {
+              type: "string",
+              enum: ["causes", "enables", "prevents", "precedes", "follows"],
+              description: "Type of temporal relation"
+            },
+            strength: {
+              type: "number",
+              minimum: 0,
+              maximum: 1,
+              description: "Relation strength (0-1)"
+            },
+            delay: { type: "number", description: "Optional time delay between events" }
+          },
+          required: ["id", "from", "to", "relationType", "strength"]
+        },
+        description: "Temporal causal/enabling relations"
+      },
       action: {
         type: "string",
         enum: ["add_thought", "summarize", "export", "switch_mode", "get_session"],
@@ -215,13 +380,20 @@ Choose the mode that best fits your problem type.`,
       },
       newMode: {
         type: "string",
-        enum: ["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical"],
+        enum: ["sequential", "shannon", "mathematics", "physics", "hybrid", "abductive", "causal", "bayesian", "counterfactual", "analogical", "temporal", "gametheory", "evidential"],
         description: "New mode for switch_mode action"
       }
     },
     required: ["thought", "thoughtNumber", "totalThoughts", "nextThoughtNeeded"]
   }
 };
+
+// src/types/modes/temporal.ts
+function isTemporalThought(thought) {
+  return thought.mode === "temporal";
+}
+
+// src/session/manager.ts
 var DEFAULT_CONFIG = {
   modeConfig: {
     mode: "hybrid" /* HYBRID */,
@@ -393,12 +565,30 @@ var SessionManager = class {
       const thoughtsWithUncertainty = session.thoughts.filter((t) => "uncertainty" in t).length;
       metrics.averageUncertainty = thoughtsWithUncertainty > 0 ? totalUncertainty / thoughtsWithUncertainty : 0;
     }
-    if ("dependencies" in thought) {
+    if ("dependencies" in thought && thought.dependencies) {
       const deps = thought.dependencies;
-      if (deps.length > metrics.dependencyDepth) {
+      if (deps && deps.length > metrics.dependencyDepth) {
         metrics.dependencyDepth = deps.length;
       }
     }
+    if (isTemporalThought(thought)) {
+      if (thought.events) {
+        metrics.customMetrics.set("totalEvents", thought.events.length);
+      }
+      if (thought.timeline) {
+        metrics.customMetrics.set("timelineUnit", thought.timeline.timeUnit);
+      }
+      if (thought.relations) {
+        const causalRelations = thought.relations.filter((r) => r.relationType === "causes");
+        metrics.customMetrics.set("causalRelations", causalRelations.length);
+      }
+      if (thought.constraints) {
+        metrics.customMetrics.set("temporalConstraints", thought.constraints.length);
+      }
+      if (thought.intervals) {
+        metrics.customMetrics.set("timeIntervals", thought.intervals.length);
+      }
+    }
   }
 };
 

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* Unified thinking tool for DeepThinking MCP v2.0\n * Supports 10 thinking modes\n */\n\nimport { z } from 'zod';\n\n/**\n * Zod schema for runtime validation (internal use)\n */\nexport const ThinkingToolSchema = z.object({\n  sessionId: z.string().optional(),\n  mode: z.enum(['sequential', 'shannon', 'mathematics', 'physics', 'hybrid', 'abductive', 'causal', 'bayesian', 'counterfactual', 'analogical']).default('hybrid'),\n  thought: z.string(),\n  thoughtNumber: z.number().int().positive(),\n  totalThoughts: z.number().int().positive(),\n  nextThoughtNeeded: z.boolean(),\n  isRevision: z.boolean().optional(),\n  revisesThought: z.string().optional(),\n  revisionReason: z.string().optional(),\n  branchFrom: z.string().optional(),\n  branchId: z.string().optional(),\n  stage: z.enum(['problem_definition', 'constraints', 'model', 'proof', 'implementation']).optional(),\n  uncertainty: z.number().min(0).max(1).optional(),\n  dependencies: z.array(z.string()).optional(),\n  assumptions: 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analysis\n- analogical: Cross-domain pattern matching and insights\n\nChoose the mode that best fits your problem type.`,\n  inputSchema: {\n    type: \"object\",\n    properties: {\n      sessionId: {\n        type: \"string\",\n        description: \"Session ID (creates new if omitted)\"\n      },\n      mode: {\n        type: \"string\",\n        enum: [\"sequential\", \"shannon\", \"mathematics\", \"physics\", \"hybrid\", \"abductive\", \"causal\", \"bayesian\", \"counterfactual\", \"analogical\"],\n        description: \"Thinking mode to use\"\n      },\n      thought: {\n        type: \"string\",\n        description: \"The thought content\"\n      },\n      thoughtNumber: {\n        type: \"integer\",\n        minimum: 1,\n        description: \"Position in sequence\"\n      },\n      totalThoughts: {\n        type: \"integer\",\n        minimum: 1,\n        description: \"Estimated total thoughts\"\n      },\n      nextThoughtNeeded: {\n        type: \"boolean\",\n        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physicalInterpretation: {\n        type: \"object\",\n        properties: {\n          quantity: { type: \"string\" },\n          units: { type: \"string\" },\n          conservationLaws: {\n            type: \"array\",\n            items: { type: \"string\" }\n          }\n        },\n        required: [\"quantity\", \"units\", \"conservationLaws\"]\n      },\n      action: {\n        type: \"string\",\n        enum: [\"add_thought\", \"summarize\", \"export\", \"switch_mode\", \"get_session\"],\n        description: \"Action to perform\"\n      },\n      exportFormat: {\n        type: \"string\",\n        enum: [\"markdown\", \"latex\", \"json\", \"html\", \"jupyter\"],\n        description: \"Export format\"\n      },\n      newMode: {\n        type: \"string\",\n        enum: [\"sequential\", \"shannon\", \"mathematics\", \"physics\", \"hybrid\", \"abductive\", \"causal\", \"bayesian\", \"counterfactual\", \"analogical\"],\n        description: \"New mode for switch_mode action\"\n 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private config: Partial<SessionConfig>;\n\n  constructor(config?: Partial<SessionConfig>) {\n    this.activeSessions = new Map();\n    this.config = config || {};\n  }\n\n  /**\n   * Create a new thinking session\n   */\n  async createSession(options: {\n    title?: string;\n    mode?: ThinkingMode;\n    domain?: string;\n    author?: string;\n    config?: Partial<SessionConfig>;\n  } = {}): Promise<ThinkingSession> {\n    const sessionId = randomUUID();\n    const now = new Date();\n\n    const session: ThinkingSession = {\n      id: sessionId,\n      title: options.title || 'Untitled Session',\n      mode: options.mode || ThinkingMode.HYBRID,\n      domain: options.domain,\n      config: this.mergeConfig(options.config),\n      thoughts: [],\n      createdAt: now,\n      updatedAt: now,\n      author: options.author,\n      currentThoughtNumber: 0,\n      isComplete: false,\n      metrics: this.initializeMetrics(),\n      tags: [],\n      collaborators: options.author ? [options.author] : []\n    };\n\n    this.activeSessions.set(sessionId, session);\n    return session;\n  }\n\n  /**\n   * Get a session by ID\n   */\n  async getSession(sessionId: string): Promise<ThinkingSession | null> {\n    return this.activeSessions.get(sessionId) || null;\n  }\n\n  /**\n   * Add a thought to a session\n   */\n  async addThought(sessionId: string, thought: Thought): Promise<ThinkingSession> {\n    const session = this.activeSessions.get(sessionId);\n    if (!session) {\n      throw new Error(`Session ${sessionId} not found`);\n    }\n\n    // Update thought with session metadata\n    thought.sessionId = sessionId;\n    thought.timestamp = new Date();\n\n    // Add thought to session\n    session.thoughts.push(thought);\n    session.currentThoughtNumber = thought.thoughtNumber;\n    session.updatedAt = new Date();\n\n    // Update metrics\n    this.updateMetrics(session, thought);\n\n    // Check if session is complete\n    if (!thought.nextThoughtNeeded) {\n      session.isComplete = true;\n    }\n\n    return session;\n  }\n\n  /**\n   * Update session mode\n   */\n  async switchMode(\n    sessionId: string,\n    newMode: ThinkingMode,\n    reason?: string\n  ): Promise<ThinkingSession> {\n    const session = this.activeSessions.get(sessionId);\n    if (!session) {\n      throw new Error(`Session ${sessionId} not found`);\n    }\n\n    const oldMode = session.mode;\n    session.mode = newMode;\n    session.config.modeConfig.mode = newMode;\n    session.updatedAt = new Date();\n\n    return session;\n  }\n\n  /**\n   * List all sessions\n   */\n  async listSessions(): Promise<SessionMetadata[]> {\n    return Array.from(this.activeSessions.values()).map(session => ({\n      id: session.id,\n      title: session.title,\n      createdAt: session.createdAt,\n      updatedAt: session.updatedAt,\n      thoughtCount: session.thoughts.length,\n      mode: session.mode,\n      isComplete: session.isComplete\n    }));\n  }\n\n  /**\n   * Delete a session\n   */\n  async deleteSession(sessionId: string): Promise<void> {\n    this.activeSessions.delete(sessionId);\n  }\n\n  /**\n   * Generate summary of session\n   */\n  async generateSummary(sessionId: string): Promise<string> {\n    const session = this.activeSessions.get(sessionId);\n    if (!session) {\n      throw new Error(`Session ${sessionId} not found`);\n    }\n\n    let summary = `# ${session.title}\\n\\n`;\n    summary += `Mode: ${session.mode}\\n`;\n    summary += `Total Thoughts: ${session.thoughts.length}\\n`;\n    summary += `Status: ${session.isComplete ? 'Complete' : 'In Progress'}\\n\\n`;\n\n    summary += `## Key Thoughts:\\n\\n`;\n    for (const thought of session.thoughts) {\n      summary += `${thought.thoughtNumber}. ${thought.content.substring(0, 100)}...\\n`;\n    }\n\n    return summary;\n  }\n\n  /**\n   * Merge configurations\n   */\n  private mergeConfig(userConfig?: Partial<SessionConfig>): SessionConfig {\n    return {\n      ...DEFAULT_CONFIG,\n      ...this.config,\n      ...userConfig\n    } as SessionConfig;\n  }\n\n  /**\n   * Initialize metrics\n   */\n  private initializeMetrics(): SessionMetrics {\n    return {\n      totalThoughts: 0,\n      thoughtsByType: {},\n      averageUncertainty: 0,\n      revisionCount: 0,\n      timeSpent: 0,\n      dependencyDepth: 0\n    };\n  }\n\n  /**\n   * Update session metrics\n   */\n  private updateMetrics(session: ThinkingSession, thought: Thought): void {\n    const metrics = session.metrics;\n\n    // Update total thoughts\n    metrics.totalThoughts = session.thoughts.length;\n\n    // Update revision count\n    if (thought.isRevision) {\n      metrics.revisionCount++;\n    }\n\n    // Update time spent (in milliseconds)\n    metrics.timeSpent = session.updatedAt.getTime() - session.createdAt.getTime();\n\n    // Update average uncertainty (for modes that have uncertainty)\n    if ('uncertainty' in thought) {\n      const totalUncertainty = session.thoughts\n        .filter(t => 'uncertainty' in t)\n        .reduce((sum, t) => sum + (t as any).uncertainty, 0);\n      const thoughtsWithUncertainty = session.thoughts.filter(t => 'uncertainty' in t).length;\n      metrics.averageUncertainty = thoughtsWithUncertainty > 0\n        ? totalUncertainty / thoughtsWithUncertainty\n        : 0;\n    }\n\n    // Update dependency depth\n    if ('dependencies' in thought) {\n      const deps = (thought as any).dependencies as string[];\n      if (deps.length > metrics.dependencyDepth) {\n        metrics.dependencyDepth = deps.length;\n      }\n    }\n  }\n}\n","#!/usr/bin/env node\n\n/**\n * DeepThinking MCP Server\n * Unified deep thinking server combining sequential, Shannon, and mathematical reasoning\n */\n\nimport { Server } from '@modelcontextprotocol/sdk/server/index.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport {\n  CallToolRequestSchema,\n  ListToolsRequestSchema,\n} from '@modelcontextprotocol/sdk/types.js';\nimport { randomUUID } from 'crypto';\n\nimport { thinkingTool, ThinkingToolInput, ThinkingToolSchema } from './tools/thinking.js';\nimport { SessionManager } from './session/index.js';\nimport {\n  ThinkingMode,\n  ShannonStage,\n  SequentialThought,\n  ShannonThought,\n  MathematicsThought,\n  PhysicsThought,\n  HybridThought,\n} from './types/index.js';\n\nconst server = new Server(\n  {\n    name: 'deepthinking-mcp',\n    version: '1.0.0',\n  },\n  {\n    capabilities: {\n      tools: {},\n    },\n  }\n);\n\nconst sessionManager = new SessionManager();\n\nserver.setRequestHandler(ListToolsRequestSchema, async () => {\n  return {\n    tools: [thinkingTool],\n  };\n});\n\nserver.setRequestHandler(CallToolRequestSchema, async (request) => {\n  const { name, arguments: args } = request.params;\n\n  if (name === 'deepthinking') {\n    try {\n      const input = ThinkingToolSchema.parse(args) as ThinkingToolInput;\n\n      switch (input.action) {\n        case 'add_thought':\n          return await handleAddThought(input);\n        case 'summarize':\n          return await handleSummarize(input);\n        case 'export':\n          return await handleExport(input);\n        case 'switch_mode':\n          return await handleSwitchMode(input);\n        case 'get_session':\n          return await handleGetSession(input);\n        default:\n          throw new Error(`Unknown action: ${input.action}`);\n      }\n    } catch (error) {\n      return {\n        content: [\n          {\n            type: 'text',\n            text: `Error: ${error instanceof Error ? error.message : String(error)}`,\n          },\n        ],\n        isError: true,\n      };\n    }\n  }\n\n  throw new Error(`Unknown tool: ${name}`);\n});\n\nasync function handleAddThought(input: ThinkingToolInput) {\n  let sessionId = input.sessionId;\n  if (!sessionId) {\n    const session = await sessionManager.createSession({\n      mode: input.mode as ThinkingMode,\n      title: `Thinking Session ${new Date().toISOString()}`,\n    });\n    sessionId = session.id;\n  }\n\n  const thought = createThought(input, sessionId);\n  const session = await sessionManager.addThought(sessionId, thought);\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: JSON.stringify({\n          sessionId: session.id,\n          thoughtId: thought.id,\n          thoughtNumber: thought.thoughtNumber,\n          mode: thought.mode,\n          nextThoughtNeeded: thought.nextThoughtNeeded,\n          sessionComplete: session.isComplete,\n          totalThoughts: session.thoughts.length,\n        }, null, 2),\n      },\n    ],\n  };\n}\n\nasync function handleSummarize(input: ThinkingToolInput) {\n  if (!input.sessionId) {\n    throw new Error('sessionId required for summarize action');\n  }\n\n  const summary = await sessionManager.generateSummary(input.sessionId);\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: summary,\n      },\n    ],\n  };\n}\n\nasync function handleExport(input: ThinkingToolInput) {\n  if (!input.sessionId) {\n    throw new Error('sessionId required for export action');\n  }\n\n  const session = await sessionManager.getSession(input.sessionId);\n  if (!session) {\n    throw new Error(`Session ${input.sessionId} not found`);\n  }\n\n  const exported = JSON.stringify(session, null, 2);\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: exported,\n      },\n    ],\n  };\n}\n\nasync function handleSwitchMode(input: ThinkingToolInput) {\n  if (!input.sessionId || !input.newMode) {\n    throw new Error('sessionId and newMode required for switch_mode action');\n  }\n\n  const session = await sessionManager.switchMode(\n    input.sessionId,\n    input.newMode as ThinkingMode,\n    'User requested mode switch'\n  );\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: `Switched session ${session.id} to ${session.mode} mode`,\n      },\n    ],\n  };\n}\n\nasync function handleGetSession(input: ThinkingToolInput) {\n  if (!input.sessionId) {\n    throw new Error('sessionId required for get_session action');\n  }\n\n  const session = await sessionManager.getSession(input.sessionId);\n  if (!session) {\n    throw new Error(`Session ${input.sessionId} not found`);\n  }\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: JSON.stringify({\n          id: session.id,\n          title: session.title,\n          mode: session.mode,\n          thoughtCount: session.thoughts.length,\n          isComplete: session.isComplete,\n          metrics: session.metrics,\n        }, null, 2),\n      },\n    ],\n  };\n}\n\nfunction createThought(input: ThinkingToolInput, sessionId: string) {\n  const baseThought = {\n    id: randomUUID(),\n    sessionId,\n    thoughtNumber: input.thoughtNumber,\n    totalThoughts: input.totalThoughts,\n    content: input.thought,\n    timestamp: new Date(),\n    nextThoughtNeeded: input.nextThoughtNeeded,\n    isRevision: input.isRevision,\n    revisesThought: input.revisesThought,\n  };\n\n  switch (input.mode) {\n    case 'sequential':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.SEQUENTIAL,\n        revisionReason: input.revisionReason,\n        branchFrom: input.branchFrom,\n        branchId: input.branchId,\n      } as SequentialThought;\n\n    case 'shannon':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.SHANNON,\n        stage: (input.stage as ShannonStage) || ShannonStage.PROBLEM_DEFINITION,\n        uncertainty: input.uncertainty || 0.5,\n        dependencies: input.dependencies || [],\n        assumptions: input.assumptions || [],\n      } as ShannonThought;\n\n    case 'mathematics':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.MATHEMATICS,\n        thoughtType: input.thoughtType as any,\n        mathematicalModel: input.mathematicalModel,\n        proofStrategy: input.proofStrategy,\n        dependencies: input.dependencies || [],\n        assumptions: input.assumptions || [],\n        uncertainty: input.uncertainty || 0.5,\n      } as MathematicsThought;\n\n    case 'physics':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.PHYSICS,\n        thoughtType: input.thoughtType as any,\n        tensorProperties: input.tensorProperties,\n        physicalInterpretation: input.physicalInterpretation,\n        dependencies: input.dependencies || [],\n        assumptions: input.assumptions || [],\n        uncertainty: input.uncertainty || 0.5,\n      } as PhysicsThought;\n\n    case 'hybrid':\n    default:\n      return {\n        ...baseThought,\n        mode: ThinkingMode.HYBRID,\n        thoughtType: input.thoughtType as any,\n        stage: input.stage as ShannonStage,\n        uncertainty: input.uncertainty,\n        dependencies: input.dependencies,\n        assumptions: input.assumptions,\n        mathematicalModel: input.mathematicalModel,\n        tensorProperties: input.tensorProperties,\n        physicalInterpretation: input.physicalInterpretation,\n        primaryMode: input.mode as any,\n        secondaryFeatures: [],\n      } as HybridThought;\n  }\n}\n\nasync function main() {\n  const transport = new StdioServerTransport();\n  await server.connect(transport);\n  console.error('DeepThinking MCP server running on stdio');\n}\n\nmain().catch((error) => {\n  console.error('Fatal error:', error);\n  process.exit(1);\n});\n"]}
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 timeUnit: z.enum(['milliseconds', 'seconds', 'minutes', 'hours', 'days', 'months', 'years']),\n    startTime: z.number().optional(),\n    endTime: z.number().optional(),\n    events: z.array(z.string()),\n  }).optional(),\n  events: z.array(z.object({\n    id: z.string(),\n    name: z.string(),\n    description: z.string(),\n    timestamp: z.number(),\n    duration: z.number().optional(),\n    type: z.enum(['instant', 'interval']),\n    properties: z.record(z.any()),\n  })).optional(),\n  intervals: z.array(z.object({\n    id: z.string(),\n    name: z.string(),\n    start: z.number(),\n    end: z.number(),\n    overlaps: z.array(z.string()).optional(),\n    contains: z.array(z.string()).optional(),\n  })).optional(),\n  constraints: z.array(z.object({\n    id: z.string(),\n    type: z.enum(['before', 'after', 'during', 'overlaps', 'meets', 'starts', 'finishes', 'equals']),\n    subject: z.string(),\n    object: z.string(),\n    confidence: z.number().min(0).max(1),\n  })).optional(),\n  relations: z.array(z.object({\n    id: z.string(),\n    from: z.string(),\n    to: z.string(),\n    relationType: z.enum(['causes', 'enables', 'prevents', 'precedes', 'follows']),\n    strength: z.number().min(0).max(1),\n    delay: z.number().optional(),\n  })).optional(),\n  action: z.enum(['add_thought', 'summarize', 'export', 'switch_mode', 'get_session']).default('add_thought'),\n  exportFormat: z.enum(['markdown', 'latex', 'json', 'html', 'jupyter']).optional(),\n  newMode: z.enum(['sequential', 'shannon', 'mathematics', 'physics', 'hybrid', 'abductive', 'causal', 'bayesian', 'counterfactual', 'analogical', 'temporal', 'gametheory', 'evidential']).optional(),\n});\n\nexport type ThinkingToolInput = z.infer<typeof ThinkingToolSchema>;\n\n/**\n * Tool definition using plain JSON Schema (MCP standard format)\n */\nexport const thinkingTool = {\n  name: 'deepthinking',\n  description: `Advanced deep thinking tool supporting 13 reasoning modes:\n\nCore Modes:\n- sequential: Iterative refinement and exploration\n- shannon: Systematic 5-stage problem-solving\n- mathematics: Theorem proving and symbolic reasoning\n- physics: Tensor mathematics and field theory\n- hybrid: Intelligently combines multiple approaches\n\nAdvanced Modes (v2.0):\n- abductive: Inference to the best explanation, hypothesis generation\n- causal: Cause-effect analysis with causal graphs\n- bayesian: Probabilistic reasoning with evidence updates\n- counterfactual: What-if scenario analysis\n- analogical: Cross-domain pattern matching and insights\n\nPhase 3 Modes (v2.1+):\n- temporal: Event timelines, temporal constraints, causal relations over time\n- gametheory: Nash equilibria, strategic analysis, payoff matrices\n- evidential: Dempster-Shafer theory, belief functions, evidence combination\n\nChoose the mode that best fits your problem type.`,\n  inputSchema: {\n    type: \"object\",\n    properties: {\n      sessionId: {\n        type: \"string\",\n        description: \"Session ID (creates new if omitted)\"\n      },\n      mode: {\n        type: \"string\",\n        enum: [\"sequential\", \"shannon\", \"mathematics\", \"physics\", \"hybrid\", \"abductive\", \"causal\", \"bayesian\", \"counterfactual\", \"analogical\", \"temporal\", \"gametheory\", \"evidential\"],\n        description: \"Thinking mode to use\"\n      },\n      thought: {\n        type: \"string\",\n        description: \"The thought content\"\n      },\n      thoughtNumber: {\n        type: \"integer\",\n        minimum: 1,\n        description: \"Position in sequence\"\n      },\n      totalThoughts: {\n        type: \"integer\",\n        minimum: 1,\n        description: \"Estimated total thoughts\"\n      },\n      nextThoughtNeeded: {\n        type: \"boolean\",\n        description: \"Should thinking continue?\"\n      },\n      isRevision: {\n        type: \"boolean\",\n        description: \"Whether this revises previous thinking\"\n      },\n      revisesThought: {\n        type: \"string\",\n        description: \"Which thought is being reconsidered\"\n      },\n      revisionReason: {\n        type: \"string\",\n        description: \"Reason for revision\"\n      },\n      branchFrom: {\n        type: \"string\",\n        description: \"Branching point thought\"\n      },\n      branchId: {\n        type: \"string\",\n        description: \"Branch identifier\"\n      },\n      stage: {\n        type: \"string\",\n        enum: [\"problem_definition\", \"constraints\", \"model\", \"proof\", \"implementation\"],\n        description: \"Shannon methodology stage\"\n      },\n      uncertainty: {\n        type: \"number\",\n        minimum: 0,\n        maximum: 1,\n        description: \"Uncertainty level (0-1)\"\n      },\n      dependencies: {\n        type: \"array\",\n        items: { type: \"string\" },\n        description: \"Dependencies on other thoughts\"\n      },\n      assumptions: {\n        type: \"array\",\n        items: { type: \"string\" },\n        description: \"Assumptions made\"\n      },\n      thoughtType: {\n        type: \"string\",\n        description: \"Type of mathematical thought\"\n      },\n      mathematicalModel: {\n        type: \"object\",\n        properties: {\n          latex: { type: \"string\", description: \"LaTeX representation\" },\n          symbolic: { type: \"string\", description: \"Symbolic representation\" },\n          ascii: { type: \"string\", description: \"ASCII representation\" }\n        },\n        required: [\"latex\", \"symbolic\"]\n      },\n      proofStrategy: {\n        type: \"object\",\n        properties: {\n          type: {\n            type: \"string\",\n            enum: [\"direct\", \"contradiction\", \"induction\", \"construction\", \"contrapositive\"]\n          },\n          steps: {\n            type: \"array\",\n            items: { type: \"string\" }\n          }\n        },\n        required: [\"type\", \"steps\"]\n      },\n      tensorProperties: {\n        type: \"object\",\n        properties: {\n          rank: {\n            type: \"array\",\n            items: { type: \"number\" },\n            minItems: 2,\n            maxItems: 2\n          },\n          components: { type: \"string\" },\n          latex: { type: \"string\" },\n          symmetries: {\n            type: \"array\",\n            items: { type: \"string\" }\n          },\n          invariants: {\n            type: \"array\",\n            items: { type: \"string\" }\n          },\n          transformation: {\n            type: \"string\",\n            enum: [\"covariant\", \"contravariant\", \"mixed\"]\n          }\n        },\n        required: [\"rank\", \"components\", \"latex\", \"symmetries\", \"invariants\", \"transformation\"]\n      },\n      physicalInterpretation: {\n        type: \"object\",\n        properties: {\n          quantity: { type: \"string\" },\n          units: { type: \"string\" },\n          conservationLaws: {\n            type: \"array\",\n            items: { type: \"string\" }\n          }\n        },\n        required: [\"quantity\", \"units\", \"conservationLaws\"]\n      },\n      // Temporal reasoning properties (Phase 3, v2.1)\n      timeline: {\n        type: \"object\",\n        properties: {\n          id: { type: \"string\" },\n          name: { type: \"string\" },\n          timeUnit: {\n            type: \"string\",\n            enum: [\"milliseconds\", \"seconds\", \"minutes\", \"hours\", \"days\", \"months\", \"years\"],\n            description: \"Time unit for the timeline\"\n          },\n          startTime: { type: \"number\", description: \"Optional start time\" },\n          endTime: { type: \"number\", description: \"Optional end time\" },\n          events: {\n            type: \"array\",\n            items: { type: \"string\" },\n            description: \"Event IDs in this timeline\"\n          }\n        },\n        required: [\"id\", \"name\", \"timeUnit\", \"events\"],\n        description: \"Timeline structure for temporal reasoning\"\n      },\n      events: {\n        type: \"array\",\n        items: {\n          type: \"object\",\n          properties: {\n            id: { type: \"string\" },\n            name: { type: \"string\" },\n            description: { type: \"string\" },\n            timestamp: { type: \"number\", description: \"Event timestamp\" },\n            duration: { type: \"number\", description: \"Duration for interval events\" },\n            type: {\n              type: \"string\",\n              enum: [\"instant\", \"interval\"],\n              description: \"Event type\"\n            },\n            properties: {\n              type: \"object\",\n              description: \"Additional event properties\"\n            }\n          },\n          required: [\"id\", \"name\", \"description\", \"timestamp\", \"type\", \"properties\"]\n        },\n        description: \"Temporal events\"\n      },\n      intervals: {\n        type: \"array\",\n        items: {\n          type: \"object\",\n          properties: {\n            id: { type: \"string\" },\n            name: { type: \"string\" },\n            start: { type: \"number\", description: \"Interval start time\" },\n            end: { type: \"number\", description: \"Interval end time\" },\n            overlaps: {\n              type: \"array\",\n              items: { type: \"string\" },\n              description: \"IDs of overlapping intervals\"\n            },\n            contains: {\n              type: \"array\",\n              items: { type: \"string\" },\n              description: \"IDs of contained intervals\"\n            }\n          },\n          required: [\"id\", \"name\", \"start\", \"end\"]\n        },\n        description: \"Time intervals with Allen's algebra relationships\"\n      },\n      constraints: {\n        type: \"array\",\n        items: {\n          type: \"object\",\n          properties: {\n            id: { type: \"string\" },\n            type: {\n              type: \"string\",\n              enum: [\"before\", \"after\", \"during\", \"overlaps\", \"meets\", \"starts\", \"finishes\", \"equals\"],\n              description: \"Allen's interval algebra constraint type\"\n            },\n            subject: { type: \"string\", description: \"Subject event/interval ID\" },\n            object: { type: \"string\", description: \"Object event/interval ID\" },\n            confidence: {\n              type: \"number\",\n              minimum: 0,\n              maximum: 1,\n              description: \"Confidence in constraint (0-1)\"\n            }\n          },\n          required: [\"id\", \"type\", \"subject\", \"object\", \"confidence\"]\n        },\n        description: \"Temporal constraints using Allen's interval algebra\"\n      },\n      relations: {\n        type: \"array\",\n        items: {\n          type: \"object\",\n          properties: {\n            id: { type: \"string\" },\n            from: { type: \"string\", description: \"Source event ID\" },\n            to: { type: \"string\", description: \"Target event ID\" },\n            relationType: {\n              type: \"string\",\n              enum: [\"causes\", \"enables\", \"prevents\", \"precedes\", \"follows\"],\n              description: \"Type of temporal relation\"\n            },\n            strength: {\n              type: \"number\",\n              minimum: 0,\n              maximum: 1,\n              description: \"Relation strength (0-1)\"\n            },\n            delay: { type: \"number\", description: \"Optional time delay between events\" }\n          },\n          required: [\"id\", \"from\", \"to\", \"relationType\", \"strength\"]\n        },\n        description: \"Temporal causal/enabling relations\"\n      },\n      action: {\n        type: \"string\",\n        enum: [\"add_thought\", \"summarize\", \"export\", \"switch_mode\", \"get_session\"],\n        description: \"Action to perform\"\n      },\n      exportFormat: {\n        type: \"string\",\n        enum: [\"markdown\", \"latex\", \"json\", \"html\", \"jupyter\"],\n        description: \"Export format\"\n      },\n      newMode: {\n        type: \"string\",\n        enum: [\"sequential\", \"shannon\", \"mathematics\", \"physics\", \"hybrid\", \"abductive\", \"causal\", \"bayesian\", \"counterfactual\", \"analogical\", \"temporal\", \"gametheory\", \"evidential\"],\n        description: \"New mode for switch_mode action\"\n      }\n    },\n    required: [\"thought\", \"thoughtNumber\", \"totalThoughts\", \"nextThoughtNeeded\"]\n  }\n};\n","/**\n * Temporal Reasoning Mode - Type Definitions\n * Phase 3 (v2.1) - Temporal reasoning with events, intervals, constraints, and causal relations\n */\n\nimport { BaseThought } from '../core.js';\n\n/**\n * Temporal thought extends base thought with time-dependent reasoning\n */\nexport interface TemporalThought extends BaseThought {\n  mode: 'temporal';\n  thoughtType:\n    | 'event_definition'\n    | 'interval_analysis'\n    | 'temporal_constraint'\n    | 'sequence_construction'\n    | 'causality_timeline';\n\n  timeline?: Timeline;\n  events?: TemporalEvent[];\n  intervals?: TimeInterval[];\n  constraints?: TemporalConstraint[];\n  relations?: TemporalRelation[];\n}\n\n/**\n * Timeline structure organizing temporal events\n */\nexport interface Timeline {\n  id: string;\n  name: string;\n  timeUnit: 'milliseconds' | 'seconds' | 'minutes' | 'hours' | 'days' | 'months' | 'years';\n  startTime?: number;\n  endTime?: number;\n  events: string[]; // Event IDs\n}\n\n/**\n * Temporal event - either instant or interval\n */\nexport interface TemporalEvent {\n  id: string;\n  name: string;\n  description: string;\n  timestamp: number;\n  duration?: number; // For interval events\n  type: 'instant' | 'interval';\n  properties: Record<string, any>;\n}\n\n/**\n * Time interval with Allen's algebra relationships\n */\nexport interface TimeInterval {\n  id: string;\n  name: string;\n  start: number;\n  end: number;\n  overlaps?: string[]; // IDs of overlapping intervals\n  contains?: string[]; // IDs of contained intervals\n}\n\n/**\n * Temporal constraint using Allen's interval algebra\n */\nexport interface TemporalConstraint {\n  id: string;\n  type: 'before' | 'after' | 'during' | 'overlaps' | 'meets' | 'starts' | 'finishes' | 'equals';\n  subject: string; // Event/Interval ID\n  object: string; // Event/Interval ID\n  confidence: number; // 0-1\n}\n\n/**\n * Temporal relation showing causal/enabling relationships over time\n */\nexport interface TemporalRelation {\n  id: string;\n  from: string; // Event ID\n  to: string; // Event ID\n  relationType: 'causes' | 'enables' | 'prevents' | 'precedes' | 'follows';\n  strength: number; // 0-1\n  delay?: number; // Time delay between events\n}\n\n/**\n * Type guard for temporal thoughts\n */\nexport function isTemporalThought(thought: BaseThought): thought is TemporalThought {\n  return thought.mode === 'temporal';\n}\n","/**\n * Session Manager for DeepThinking MCP\n * Manages thinking sessions, persistence, and analytics\n */\n\nimport { randomUUID } from 'crypto';\nimport {\n  ThinkingSession,\n  SessionConfig,\n  SessionMetrics,\n  SessionMetadata,\n  Thought,\n  ThinkingMode,\n  ExportFormat\n} from '../types/index.js';\nimport { TemporalThought, isTemporalThought } from '../types/modes/temporal.js';\n\n/**\n * Default session configuration\n */\nconst DEFAULT_CONFIG: SessionConfig = {\n  modeConfig: {\n    mode: ThinkingMode.HYBRID,\n    strictValidation: false,\n    allowModeSwitch: true\n  },\n  enableAutoSave: true,\n  enableValidation: true,\n  enableVisualization: true,\n  integrations: {},\n  exportFormats: ['markdown', 'latex', 'json'],\n  autoExportOnComplete: false,\n  maxThoughtsInMemory: 1000,\n  compressionThreshold: 500\n};\n\n/**\n * Session Manager\n */\nexport class SessionManager {\n  private activeSessions: Map<string, ThinkingSession>;\n  private config: Partial<SessionConfig>;\n\n  constructor(config?: Partial<SessionConfig>) {\n    this.activeSessions = new Map();\n    this.config = config || {};\n  }\n\n  /**\n   * Create a new thinking session\n   */\n  async createSession(options: {\n    title?: string;\n    mode?: ThinkingMode;\n    domain?: string;\n    author?: string;\n    config?: Partial<SessionConfig>;\n  } = {}): Promise<ThinkingSession> {\n    const sessionId = randomUUID();\n    const now = new Date();\n\n    const session: ThinkingSession = {\n      id: sessionId,\n      title: options.title || 'Untitled Session',\n      mode: options.mode || ThinkingMode.HYBRID,\n      domain: options.domain,\n      config: this.mergeConfig(options.config),\n      thoughts: [],\n      createdAt: now,\n      updatedAt: now,\n      author: options.author,\n      currentThoughtNumber: 0,\n      isComplete: false,\n      metrics: this.initializeMetrics(),\n      tags: [],\n      collaborators: options.author ? [options.author] : []\n    };\n\n    this.activeSessions.set(sessionId, session);\n    return session;\n  }\n\n  /**\n   * Get a session by ID\n   */\n  async getSession(sessionId: string): Promise<ThinkingSession | null> {\n    return this.activeSessions.get(sessionId) || null;\n  }\n\n  /**\n   * Add a thought to a session\n   */\n  async addThought(sessionId: string, thought: Thought): Promise<ThinkingSession> {\n    const session = this.activeSessions.get(sessionId);\n    if (!session) {\n      throw new Error(`Session ${sessionId} not found`);\n    }\n\n    // Update thought with session metadata\n    thought.sessionId = sessionId;\n    thought.timestamp = new Date();\n\n    // Add thought to session\n    session.thoughts.push(thought);\n    session.currentThoughtNumber = thought.thoughtNumber;\n    session.updatedAt = new Date();\n\n    // Update metrics\n    this.updateMetrics(session, thought);\n\n    // Check if session is complete\n    if (!thought.nextThoughtNeeded) {\n      session.isComplete = true;\n    }\n\n    return session;\n  }\n\n  /**\n   * Update session mode\n   */\n  async switchMode(\n    sessionId: string,\n    newMode: ThinkingMode,\n    reason?: string\n  ): Promise<ThinkingSession> {\n    const session = this.activeSessions.get(sessionId);\n    if (!session) {\n      throw new Error(`Session ${sessionId} not found`);\n    }\n\n    const oldMode = session.mode;\n    session.mode = newMode;\n    session.config.modeConfig.mode = newMode;\n    session.updatedAt = new Date();\n\n    return session;\n  }\n\n  /**\n   * List all sessions\n   */\n  async listSessions(): Promise<SessionMetadata[]> {\n    return Array.from(this.activeSessions.values()).map(session => ({\n      id: session.id,\n      title: session.title,\n      createdAt: session.createdAt,\n      updatedAt: session.updatedAt,\n      thoughtCount: session.thoughts.length,\n      mode: session.mode,\n      isComplete: session.isComplete\n    }));\n  }\n\n  /**\n   * Delete a session\n   */\n  async deleteSession(sessionId: string): Promise<void> {\n    this.activeSessions.delete(sessionId);\n  }\n\n  /**\n   * Generate summary of session\n   */\n  async generateSummary(sessionId: string): Promise<string> {\n    const session = this.activeSessions.get(sessionId);\n    if (!session) {\n      throw new Error(`Session ${sessionId} not found`);\n    }\n\n    let summary = `# ${session.title}\\n\\n`;\n    summary += `Mode: ${session.mode}\\n`;\n    summary += `Total Thoughts: ${session.thoughts.length}\\n`;\n    summary += `Status: ${session.isComplete ? 'Complete' : 'In Progress'}\\n\\n`;\n\n    summary += `## Key Thoughts:\\n\\n`;\n    for (const thought of session.thoughts) {\n      summary += `${thought.thoughtNumber}. ${thought.content.substring(0, 100)}...\\n`;\n    }\n\n    return summary;\n  }\n\n  /**\n   * Merge configurations\n   */\n  private mergeConfig(userConfig?: Partial<SessionConfig>): SessionConfig {\n    return {\n      ...DEFAULT_CONFIG,\n      ...this.config,\n      ...userConfig\n    } as SessionConfig;\n  }\n\n  /**\n   * Initialize metrics\n   */\n  private initializeMetrics(): SessionMetrics {\n    return {\n      totalThoughts: 0,\n      thoughtsByType: {},\n      averageUncertainty: 0,\n      revisionCount: 0,\n      timeSpent: 0,\n      dependencyDepth: 0\n    };\n  }\n\n  /**\n   * Update session metrics\n   */\n  private updateMetrics(session: ThinkingSession, thought: Thought): void {\n    const metrics = session.metrics;\n\n    // Update total thoughts\n    metrics.totalThoughts = session.thoughts.length;\n\n    // Update revision count\n    if (thought.isRevision) {\n      metrics.revisionCount++;\n    }\n\n    // Update time spent (in milliseconds)\n    metrics.timeSpent = session.updatedAt.getTime() - session.createdAt.getTime();\n\n    // Update average uncertainty (for modes that have uncertainty)\n    if ('uncertainty' in thought) {\n      const totalUncertainty = session.thoughts\n        .filter(t => 'uncertainty' in t)\n        .reduce((sum, t) => sum + (t as any).uncertainty, 0);\n      const thoughtsWithUncertainty = session.thoughts.filter(t => 'uncertainty' in t).length;\n      metrics.averageUncertainty = thoughtsWithUncertainty > 0\n        ? totalUncertainty / thoughtsWithUncertainty\n        : 0;\n    }\n\n    // Update dependency depth\n    if ('dependencies' in thought && thought.dependencies) {\n      const deps = (thought as any).dependencies as string[];\n      if (deps && deps.length > metrics.dependencyDepth) {\n        metrics.dependencyDepth = deps.length;\n      }\n    }\n\n    // Temporal-specific metrics (Phase 3, v2.1)\n    if (isTemporalThought(thought)) {\n      if (thought.events) {\n        metrics.customMetrics.set('totalEvents', thought.events.length);\n      }\n      if (thought.timeline) {\n        metrics.customMetrics.set('timelineUnit', thought.timeline.timeUnit);\n      }\n      if (thought.relations) {\n        const causalRelations = thought.relations.filter(r => r.relationType === 'causes');\n        metrics.customMetrics.set('causalRelations', causalRelations.length);\n      }\n      if (thought.constraints) {\n        metrics.customMetrics.set('temporalConstraints', thought.constraints.length);\n      }\n      if (thought.intervals) {\n        metrics.customMetrics.set('timeIntervals', thought.intervals.length);\n      }\n    }\n  }\n}\n","#!/usr/bin/env node\n\n/**\n * DeepThinking MCP Server\n * Unified deep thinking server combining sequential, Shannon, and mathematical reasoning\n */\n\nimport { Server } from '@modelcontextprotocol/sdk/server/index.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport {\n  CallToolRequestSchema,\n  ListToolsRequestSchema,\n} from '@modelcontextprotocol/sdk/types.js';\nimport { randomUUID } from 'crypto';\n\nimport { thinkingTool, ThinkingToolInput, ThinkingToolSchema } from './tools/thinking.js';\nimport { SessionManager } from './session/index.js';\nimport {\n  ThinkingMode,\n  ShannonStage,\n  SequentialThought,\n  ShannonThought,\n  MathematicsThought,\n  PhysicsThought,\n  HybridThought,\n} from './types/index.js';\n\nconst server = new Server(\n  {\n    name: 'deepthinking-mcp',\n    version: '1.0.0',\n  },\n  {\n    capabilities: {\n      tools: {},\n    },\n  }\n);\n\nconst sessionManager = new SessionManager();\n\nserver.setRequestHandler(ListToolsRequestSchema, async () => {\n  return {\n    tools: [thinkingTool],\n  };\n});\n\nserver.setRequestHandler(CallToolRequestSchema, async (request) => {\n  const { name, arguments: args } = request.params;\n\n  if (name === 'deepthinking') {\n    try {\n      const input = ThinkingToolSchema.parse(args) as ThinkingToolInput;\n\n      switch (input.action) {\n        case 'add_thought':\n          return await handleAddThought(input);\n        case 'summarize':\n          return await handleSummarize(input);\n        case 'export':\n          return await handleExport(input);\n        case 'switch_mode':\n          return await handleSwitchMode(input);\n        case 'get_session':\n          return await handleGetSession(input);\n        default:\n          throw new Error(`Unknown action: ${input.action}`);\n      }\n    } catch (error) {\n      return {\n        content: [\n          {\n            type: 'text',\n            text: `Error: ${error instanceof Error ? error.message : String(error)}`,\n          },\n        ],\n        isError: true,\n      };\n    }\n  }\n\n  throw new Error(`Unknown tool: ${name}`);\n});\n\nasync function handleAddThought(input: ThinkingToolInput) {\n  let sessionId = input.sessionId;\n  if (!sessionId) {\n    const session = await sessionManager.createSession({\n      mode: input.mode as ThinkingMode,\n      title: `Thinking Session ${new Date().toISOString()}`,\n    });\n    sessionId = session.id;\n  }\n\n  const thought = createThought(input, sessionId);\n  const session = await sessionManager.addThought(sessionId, thought);\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: JSON.stringify({\n          sessionId: session.id,\n          thoughtId: thought.id,\n          thoughtNumber: thought.thoughtNumber,\n          mode: thought.mode,\n          nextThoughtNeeded: thought.nextThoughtNeeded,\n          sessionComplete: session.isComplete,\n          totalThoughts: session.thoughts.length,\n        }, null, 2),\n      },\n    ],\n  };\n}\n\nasync function handleSummarize(input: ThinkingToolInput) {\n  if (!input.sessionId) {\n    throw new Error('sessionId required for summarize action');\n  }\n\n  const summary = await sessionManager.generateSummary(input.sessionId);\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: summary,\n      },\n    ],\n  };\n}\n\nasync function handleExport(input: ThinkingToolInput) {\n  if (!input.sessionId) {\n    throw new Error('sessionId required for export action');\n  }\n\n  const session = await sessionManager.getSession(input.sessionId);\n  if (!session) {\n    throw new Error(`Session ${input.sessionId} not found`);\n  }\n\n  const exported = JSON.stringify(session, null, 2);\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: exported,\n      },\n    ],\n  };\n}\n\nasync function handleSwitchMode(input: ThinkingToolInput) {\n  if (!input.sessionId || !input.newMode) {\n    throw new Error('sessionId and newMode required for switch_mode action');\n  }\n\n  const session = await sessionManager.switchMode(\n    input.sessionId,\n    input.newMode as ThinkingMode,\n    'User requested mode switch'\n  );\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: `Switched session ${session.id} to ${session.mode} mode`,\n      },\n    ],\n  };\n}\n\nasync function handleGetSession(input: ThinkingToolInput) {\n  if (!input.sessionId) {\n    throw new Error('sessionId required for get_session action');\n  }\n\n  const session = await sessionManager.getSession(input.sessionId);\n  if (!session) {\n    throw new Error(`Session ${input.sessionId} not found`);\n  }\n\n  return {\n    content: [\n      {\n        type: 'text',\n        text: JSON.stringify({\n          id: session.id,\n          title: session.title,\n          mode: session.mode,\n          thoughtCount: session.thoughts.length,\n          isComplete: session.isComplete,\n          metrics: session.metrics,\n        }, null, 2),\n      },\n    ],\n  };\n}\n\nfunction createThought(input: ThinkingToolInput, sessionId: string) {\n  const baseThought = {\n    id: randomUUID(),\n    sessionId,\n    thoughtNumber: input.thoughtNumber,\n    totalThoughts: input.totalThoughts,\n    content: input.thought,\n    timestamp: new Date(),\n    nextThoughtNeeded: input.nextThoughtNeeded,\n    isRevision: input.isRevision,\n    revisesThought: input.revisesThought,\n  };\n\n  switch (input.mode) {\n    case 'sequential':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.SEQUENTIAL,\n        revisionReason: input.revisionReason,\n        branchFrom: input.branchFrom,\n        branchId: input.branchId,\n      } as SequentialThought;\n\n    case 'shannon':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.SHANNON,\n        stage: (input.stage as ShannonStage) || ShannonStage.PROBLEM_DEFINITION,\n        uncertainty: input.uncertainty || 0.5,\n        dependencies: input.dependencies || [],\n        assumptions: input.assumptions || [],\n      } as ShannonThought;\n\n    case 'mathematics':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.MATHEMATICS,\n        thoughtType: input.thoughtType as any,\n        mathematicalModel: input.mathematicalModel,\n        proofStrategy: input.proofStrategy,\n        dependencies: input.dependencies || [],\n        assumptions: input.assumptions || [],\n        uncertainty: input.uncertainty || 0.5,\n      } as MathematicsThought;\n\n    case 'physics':\n      return {\n        ...baseThought,\n        mode: ThinkingMode.PHYSICS,\n        thoughtType: input.thoughtType as any,\n        tensorProperties: input.tensorProperties,\n        physicalInterpretation: input.physicalInterpretation,\n        dependencies: input.dependencies || [],\n        assumptions: input.assumptions || [],\n        uncertainty: input.uncertainty || 0.5,\n      } as PhysicsThought;\n\n    case 'hybrid':\n    default:\n      return {\n        ...baseThought,\n        mode: ThinkingMode.HYBRID,\n        thoughtType: input.thoughtType as any,\n        stage: input.stage as ShannonStage,\n        uncertainty: input.uncertainty,\n        dependencies: input.dependencies,\n        assumptions: input.assumptions,\n        mathematicalModel: input.mathematicalModel,\n        tensorProperties: input.tensorProperties,\n        physicalInterpretation: input.physicalInterpretation,\n        primaryMode: input.mode as any,\n        secondaryFeatures: [],\n      } as HybridThought;\n  }\n}\n\nasync function main() {\n  const transport = new StdioServerTransport();\n  await server.connect(transport);\n  console.error('DeepThinking MCP server running on stdio');\n}\n\nmain().catch((error) => {\n  console.error('Fatal error:', error);\n  process.exit(1);\n});\n"]}

package/package.json

@@ -1,72 +1,73 @@
-{
-  "name": "deepthinking-mcp",
-  "version": "2.0.0",
-  "description": "Comprehensive MCP server with 10 advanced reasoning modes: Sequential, Shannon, Mathematics, Physics, Hybrid, Abductive, Causal, Bayesian, Counterfactual, and Analogical reasoning",
-  "author": "Daniel Simon Jr.",
-  "license": "MIT",
-  "type": "module",
-  "bin": {
-    "deepthinking-mcp": "./dist/index.js"
-  },
-  "main": "./dist/index.js",
-  "types": "./dist/index.d.ts",
-  "files": [
-    "dist/",
-    "README.md",
-    "LICENSE"
-  ],
-  "scripts": {
-    "build": "tsup",
-    "dev": "tsup --watch",
-    "test": "vitest",
-    "test:coverage": "vitest --coverage",
-    "lint": "eslint src/",
-    "format": "prettier --write src/",
-    "typecheck": "tsc --noEmit",
-    "prepublishOnly": "npm run build && npm test"
-  },
-  "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.0.4",
-    "zod": "^3.22.4",
-    "zod-to-json-schema": "^3.24.6"
-  },
-  "devDependencies": {
-    "@types/node": "^20.11.0",
-    "@typescript-eslint/eslint-plugin": "^6.19.0",
-    "@typescript-eslint/parser": "^6.19.0",
-    "@vitest/coverage-v8": "^1.2.0",
-    "eslint": "^8.56.0",
-    "prettier": "^3.2.4",
-    "tsup": "^8.0.1",
-    "typescript": "^5.3.3",
-    "vitest": "^1.2.0"
-  },
-  "keywords": [
-    "mcp",
-    "model-context-protocol",
-    "thinking",
-    "reasoning",
-    "sequential-thinking",
-    "shannon-thinking",
-    "physics",
-    "mathematics",
-    "tensor",
-    "deep-thinking",
-    "mathematical-reasoning",
-    "abductive-reasoning",
-    "causal-analysis",
-    "bayesian-inference",
-    "counterfactual-analysis",
-    "analogical-reasoning",
-    "causal-graphs",
-    "hypothesis-generation",
-    "probabilistic-reasoning"
-  ],
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/danielsimonjr/deepthinking-mcp"
-  },
-  "engines": {
-    "node": ">=18.0.0"
-  }
-}
+{
+  "name": "deepthinking-mcp",
+  "version": "2.1.0",
+  "description": "Comprehensive MCP server with 10 advanced reasoning modes: Sequential, Shannon, Mathematics, Physics, Hybrid, Abductive, Causal, Bayesian, Counterfactual, and Analogical reasoning",
+  "author": "Daniel Simon Jr.",
+  "license": "MIT",
+  "type": "module",
+  "bin": {
+    "deepthinking-mcp": "./dist/index.js"
+  },
+  "main": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "files": [
+    "dist/",
+    "README.md",
+    "LICENSE"
+  ],
+  "scripts": {
+    "build": "tsup",
+    "dev": "tsup --watch",
+    "test": "vitest",
+    "test:run": "vitest --run",
+    "test:coverage": "vitest --coverage",
+    "lint": "eslint src/",
+    "format": "prettier --write src/",
+    "typecheck": "tsc --noEmit",
+    "prepublishOnly": "npm run build && npm run test:run"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.0.4",
+    "zod": "^3.22.4",
+    "zod-to-json-schema": "^3.24.6"
+  },
+  "devDependencies": {
+    "@types/node": "^20.11.0",
+    "@typescript-eslint/eslint-plugin": "^6.19.0",
+    "@typescript-eslint/parser": "^6.19.0",
+    "@vitest/coverage-v8": "^1.2.0",
+    "eslint": "^8.56.0",
+    "prettier": "^3.2.4",
+    "tsup": "^8.0.1",
+    "typescript": "^5.3.3",
+    "vitest": "^1.2.0"
+  },
+  "keywords": [
+    "mcp",
+    "model-context-protocol",
+    "thinking",
+    "reasoning",
+    "sequential-thinking",
+    "shannon-thinking",
+    "physics",
+    "mathematics",
+    "tensor",
+    "deep-thinking",
+    "mathematical-reasoning",
+    "abductive-reasoning",
+    "causal-analysis",
+    "bayesian-inference",
+    "counterfactual-analysis",
+    "analogical-reasoning",
+    "causal-graphs",
+    "hypothesis-generation",
+    "probabilistic-reasoning"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/danielsimonjr/deepthinking-mcp"
+  },
+  "engines": {
+    "node": ">=18.0.0"
+  }
+}