@bis-code/deep-think 1.1.1

package/server/dist/index.js

@@ -0,0 +1,33 @@
+#!/usr/bin/env node
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { ThoughtStore } from "./engine/thought-store.js";
+import { registerThinkTool } from "./tools/think.js";
+import { registerBranchTool } from "./tools/branch.js";
+import { registerCheckpointTool } from "./tools/checkpoint.js";
+import { registerReflectTool } from "./tools/reflect.js";
+import { registerStrategizeTool } from "./tools/strategize.js";
+import { loadConfig } from "./config/loader.js";
+import { FileStore } from "./persistence/file-store.js";
+const server = new McpServer({
+    name: "mcp-deep-think",
+    version: "0.1.0",
+});
+const config = loadConfig();
+const store = new ThoughtStore(config);
+const fileStore = new FileStore(config.persistence.directory, config.persistence.maxCheckpoints);
+registerThinkTool(server, store, config, fileStore);
+registerBranchTool(server, store, config);
+registerCheckpointTool(server, store, config, fileStore);
+registerReflectTool(server, store, config);
+registerStrategizeTool(server, store, config);
+async function runServer() {
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+    console.error("mcp-deep-think server running on stdio");
+}
+runServer().catch((error) => {
+    console.error("Fatal error running server:", error);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

package/server/dist/index.js.map

@@ -0,0 +1 @@
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package/server/dist/persistence/file-store.d.ts

@@ -0,0 +1,15 @@
+import type { CheckpointData } from "../types.js";
+import type { IPersistenceAdapter } from "./types.js";
+export declare class FileStore implements IPersistenceAdapter {
+    private directory;
+    private maxCheckpoints;
+    constructor(directory: string, maxCheckpoints: number);
+    private ensureDir;
+    private filePath;
+    save(name: string, data: CheckpointData): Promise<void>;
+    load(name: string): Promise<CheckpointData | null>;
+    list(): Promise<CheckpointData[]>;
+    delete(name: string): Promise<boolean>;
+    private rotate;
+}
+//# sourceMappingURL=file-store.d.ts.map

package/server/dist/persistence/file-store.d.ts.map

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package/server/dist/persistence/file-store.js

@@ -0,0 +1,84 @@
+import { readFileSync, writeFileSync, existsSync, mkdirSync, readdirSync, unlinkSync, statSync } from "fs";
+import { join, resolve } from "path";
+export class FileStore {
+    directory;
+    maxCheckpoints;
+    constructor(directory, maxCheckpoints) {
+        this.directory = resolve(directory);
+        this.maxCheckpoints = maxCheckpoints;
+    }
+    ensureDir() {
+        if (!existsSync(this.directory)) {
+            mkdirSync(this.directory, { recursive: true });
+        }
+    }
+    filePath(name) {
+        // Sanitize name to prevent path traversal
+        const safe = name.replace(/[^a-zA-Z0-9_-]/g, "_");
+        return join(this.directory, `${safe}.json`);
+    }
+    async save(name, data) {
+        this.ensureDir();
+        const path = this.filePath(name);
+        writeFileSync(path, JSON.stringify(data, null, 2), "utf-8");
+        this.rotate();
+    }
+    async load(name) {
+        const path = this.filePath(name);
+        if (!existsSync(path))
+            return null;
+        try {
+            const raw = readFileSync(path, "utf-8");
+            return JSON.parse(raw);
+        }
+        catch {
+            return null;
+        }
+    }
+    async list() {
+        if (!existsSync(this.directory))
+            return [];
+        const files = readdirSync(this.directory)
+            .filter(f => f.endsWith(".json"))
+            .sort((a, b) => {
+            const statA = statSync(join(this.directory, a));
+            const statB = statSync(join(this.directory, b));
+            return statB.mtimeMs - statA.mtimeMs;
+        });
+        const checkpoints = [];
+        for (const file of files) {
+            try {
+                const raw = readFileSync(join(this.directory, file), "utf-8");
+                checkpoints.push(JSON.parse(raw));
+            }
+            catch {
+                // Skip corrupted files
+            }
+        }
+        return checkpoints;
+    }
+    async delete(name) {
+        const path = this.filePath(name);
+        if (!existsSync(path))
+            return false;
+        unlinkSync(path);
+        return true;
+    }
+    rotate() {
+        if (!existsSync(this.directory))
+            return;
+        const files = readdirSync(this.directory)
+            .filter(f => f.endsWith(".json"))
+            .map(f => ({
+            name: f,
+            mtime: statSync(join(this.directory, f)).mtimeMs,
+        }))
+            .sort((a, b) => b.mtime - a.mtime);
+        if (files.length > this.maxCheckpoints) {
+            for (const file of files.slice(this.maxCheckpoints)) {
+                unlinkSync(join(this.directory, file.name));
+            }
+        }
+    }
+}
+//# sourceMappingURL=file-store.js.map

package/server/dist/persistence/file-store.js.map

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package/server/dist/persistence/types.d.ts

@@ -0,0 +1,8 @@
+import type { CheckpointData } from "../types.js";
+export interface IPersistenceAdapter {
+    save(name: string, data: CheckpointData): Promise<void>;
+    load(name: string): Promise<CheckpointData | null>;
+    list(): Promise<CheckpointData[]>;
+    delete(name: string): Promise<boolean>;
+}
+//# sourceMappingURL=types.d.ts.map

package/server/dist/persistence/types.d.ts.map

@@ -0,0 +1 @@
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package/server/dist/persistence/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/server/dist/persistence/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/persistence/types.ts"],"names":[],"mappings":""}

package/server/dist/tools/branch.d.ts

@@ -0,0 +1,5 @@
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { ThoughtStore } from "../engine/thought-store.js";
+import type { DeepThinkConfig } from "../types.js";
+export declare function registerBranchTool(server: McpServer, store: ThoughtStore, _config: DeepThinkConfig): void;
+//# sourceMappingURL=branch.d.ts.map

package/server/dist/tools/branch.d.ts.map

@@ -0,0 +1 @@
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package/server/dist/tools/branch.js

@@ -0,0 +1,133 @@
+import { z } from "zod";
+import { tokenize, jaccardSimilarity } from "../engine/analyzer.js";
+export function registerBranchTool(server, store, _config) {
+    server.registerTool("branch", {
+        title: "Branch",
+        description: `Manage thought branches — create, list, compare, and merge alternative reasoning paths.
+
+Use branching when:
+- You want to explore multiple approaches in parallel
+- A decision point has several viable options
+- You need to compare trade-offs between alternatives
+
+Operations:
+- create: Start a new branch from any thought (use the think tool with branchFromThought)
+- list: Show all branches with summaries
+- compare: Compare two branches to find agreements, disagreements, and unique insights
+- merge: Synthesize branches into a conclusion, recording which approach won and why`,
+        inputSchema: {
+            operation: z.enum(["list", "compare", "merge"]).describe("Branch operation to perform"),
+            branchA: z.string().optional().describe("First branch ID (for compare/merge)"),
+            branchB: z.string().optional().describe("Second branch ID (for compare/merge)"),
+            mergeConclusion: z.string().optional().describe("Your synthesis conclusion (for merge)"),
+            winningBranch: z.string().optional().describe("Which branch's approach won (for merge)"),
+            rationale: z.string().optional().describe("Why this branch won (for merge)"),
+        },
+    }, async (args) => {
+        switch (args.operation) {
+            case "list": {
+                const branches = store.getBranches();
+                const branchInfos = Object.entries(branches).map(([id, thoughts]) => ({
+                    id,
+                    fromThought: thoughts[0]?.branchFromThought ?? 0,
+                    thoughtCount: thoughts.length,
+                    summary: thoughts.length > 0
+                        ? thoughts[thoughts.length - 1].thought.slice(0, 100) + (thoughts[thoughts.length - 1].thought.length > 100 ? "..." : "")
+                        : "(empty branch)",
+                }));
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ branches: branchInfos }, null, 2) }],
+                };
+            }
+            case "compare": {
+                if (!args.branchA || !args.branchB) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: "compare requires branchA and branchB" }],
+                    };
+                }
+                const thoughtsA = store.getBranch(args.branchA);
+                const thoughtsB = store.getBranch(args.branchB);
+                if (thoughtsA.length === 0 || thoughtsB.length === 0) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: `Branch not found: ${thoughtsA.length === 0 ? args.branchA : args.branchB}` }],
+                    };
+                }
+                const tokensA = thoughtsA.map(t => tokenize(t.thought));
+                const tokensB = thoughtsB.map(t => tokenize(t.thought));
+                const agreements = [];
+                const disagreements = [];
+                const uniqueToA = [];
+                const uniqueToB = [];
+                for (const tA of thoughtsA) {
+                    let bestSim = 0;
+                    let bestMatch = "";
+                    for (const tB of thoughtsB) {
+                        const sim = jaccardSimilarity(tokenize(tA.thought), tokenize(tB.thought));
+                        if (sim > bestSim) {
+                            bestSim = sim;
+                            bestMatch = tB.thought.slice(0, 80);
+                        }
+                    }
+                    if (bestSim > 0.4) {
+                        agreements.push(tA.thought.slice(0, 80));
+                    }
+                    else {
+                        uniqueToA.push(tA.thought.slice(0, 80));
+                    }
+                }
+                for (const tB of thoughtsB) {
+                    let bestSim = 0;
+                    for (const tA of thoughtsA) {
+                        const sim = jaccardSimilarity(tokenize(tB.thought), tokenize(tA.thought));
+                        if (sim > bestSim)
+                            bestSim = sim;
+                    }
+                    if (bestSim <= 0.4) {
+                        uniqueToB.push(tB.thought.slice(0, 80));
+                    }
+                }
+                const comparison = {
+                    branchA: args.branchA,
+                    branchB: args.branchB,
+                    agreements,
+                    disagreements,
+                    uniqueToA,
+                    uniqueToB,
+                };
+                return {
+                    content: [{ type: "text", text: JSON.stringify(comparison, null, 2) }],
+                };
+            }
+            case "merge": {
+                if (!args.mergeConclusion) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: "merge requires mergeConclusion" }],
+                    };
+                }
+                const history = store.getHistory();
+                const mergeThoughtNumber = history.length + 1;
+                store.addThought({
+                    thought: `[MERGE] ${args.mergeConclusion}`,
+                    thoughtNumber: mergeThoughtNumber,
+                    totalThoughts: mergeThoughtNumber,
+                    nextThoughtNeeded: false,
+                    tags: ["merge"],
+                });
+                const result = {
+                    mergedFrom: [args.branchA ?? "", args.branchB ?? ""].filter(Boolean),
+                    conclusion: args.mergeConclusion,
+                    winningBranch: args.winningBranch ?? null,
+                    rationale: args.rationale ?? "",
+                    mergedThoughtNumber: mergeThoughtNumber,
+                };
+                return {
+                    content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+                };
+            }
+        }
+    });
+}
+//# sourceMappingURL=branch.js.map

package/server/dist/tools/branch.js.map

@@ -0,0 +1 @@
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package/server/dist/tools/checkpoint.d.ts

@@ -0,0 +1,6 @@
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { ThoughtStore } from "../engine/thought-store.js";
+import type { DeepThinkConfig } from "../types.js";
+import { FileStore } from "../persistence/file-store.js";
+export declare function registerCheckpointTool(server: McpServer, store: ThoughtStore, config: DeepThinkConfig, fileStore: FileStore): void;
+//# sourceMappingURL=checkpoint.d.ts.map

package/server/dist/tools/checkpoint.d.ts.map

@@ -0,0 +1 @@
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package/server/dist/tools/checkpoint.js

@@ -0,0 +1,95 @@
+import { z } from "zod";
+export function registerCheckpointTool(server, store, config, fileStore) {
+    server.registerTool("checkpoint", {
+        title: "Checkpoint",
+        description: `Save and restore reasoning state. Enables persistent thinking across sessions.
+
+Use checkpoints to:
+- Save progress before exploring a risky reasoning path
+- Resume a thought chain after a session restart
+- Create snapshots at key decision points
+- Roll back to a previous state if reasoning goes off track
+
+Operations:
+- save: Snapshot the current thought chain, branches, and strategy
+- load: Restore a previously saved checkpoint
+- list: Show all available checkpoints
+- delete: Remove a checkpoint`,
+        inputSchema: {
+            operation: z.enum(["save", "load", "list", "delete"]).describe("Checkpoint operation"),
+            name: z.string().optional().describe("Checkpoint name (for save/load/delete)"),
+        },
+    }, async (args) => {
+        switch (args.operation) {
+            case "save": {
+                const name = args.name ?? `auto-${Date.now()}`;
+                const state = store.serialize();
+                const checkpoint = {
+                    name,
+                    timestamp: new Date().toISOString(),
+                    sessionId: store.getSessionId(),
+                    thoughtHistory: state.thoughtHistory,
+                    branches: state.branches,
+                    activeStrategy: state.activeStrategy,
+                    metadata: {},
+                    projectPath: process.cwd(),
+                };
+                await fileStore.save(name, checkpoint);
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ saved: name, thoughtCount: state.thoughtHistory.length }, null, 2) }],
+                };
+            }
+            case "load": {
+                if (!args.name) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: "load requires a checkpoint name" }],
+                    };
+                }
+                const checkpoint = await fileStore.load(args.name);
+                if (!checkpoint) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: `Checkpoint not found: ${args.name}` }],
+                    };
+                }
+                store.restore({
+                    thoughtHistory: checkpoint.thoughtHistory,
+                    branches: checkpoint.branches,
+                    activeStrategy: checkpoint.activeStrategy,
+                    sessionId: checkpoint.sessionId,
+                });
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ loaded: args.name, thoughtCount: checkpoint.thoughtHistory.length }, null, 2) }],
+                };
+            }
+            case "list": {
+                const checkpoints = await fileStore.list();
+                const infos = checkpoints.map(cp => ({
+                    name: cp.name,
+                    timestamp: cp.timestamp,
+                    thoughtCount: cp.thoughtHistory.length,
+                    branchCount: Object.keys(cp.branches).length,
+                    strategy: cp.activeStrategy,
+                    projectPath: cp.projectPath,
+                }));
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ checkpoints: infos }, null, 2) }],
+                };
+            }
+            case "delete": {
+                if (!args.name) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: "delete requires a checkpoint name" }],
+                    };
+                }
+                const deleted = await fileStore.delete(args.name);
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ deleted: args.name, success: deleted }, null, 2) }],
+                };
+            }
+        }
+    });
+}
+//# sourceMappingURL=checkpoint.js.map

package/server/dist/tools/checkpoint.js.map

@@ -0,0 +1 @@
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package/server/dist/tools/reflect.d.ts

@@ -0,0 +1,5 @@
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { ThoughtStore } from "../engine/thought-store.js";
+import type { DeepThinkConfig } from "../types.js";
+export declare function registerReflectTool(server: McpServer, store: ThoughtStore, config: DeepThinkConfig): void;
+//# sourceMappingURL=reflect.d.ts.map

package/server/dist/tools/reflect.d.ts.map

@@ -0,0 +1 @@
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package/server/dist/tools/reflect.js

@@ -0,0 +1,41 @@
+import { z } from "zod";
+import { Analyzer } from "../engine/analyzer.js";
+export function registerReflectTool(server, store, config) {
+    const analyzer = new Analyzer(config);
+    server.registerTool("reflect", {
+        title: "Reflect",
+        description: `Analyze the thought chain to detect patterns, issues, and gaps. This is the key differentiator from sequential thinking — it actively reads and analyzes your reasoning.
+
+Use reflect to:
+- Check if you're going in circles (circular reasoning detection)
+- Find contradictions between thoughts
+- Get a progress summary
+- Identify gaps in your analysis
+- Check your reasoning against project-specific best practices (if .deep-think.json is configured)
+
+Focus modes:
+- "all": Full analysis (default)
+- "progress": How far along and what's been covered
+- "contradictions": Find conflicting thoughts
+- "gaps": What reasoning steps are missing
+- "patterns": Detect circular reasoning, anchoring, scope creep
+
+The quality of reflection improves when thoughts include tags, confidence scores, and assumptions.`,
+        inputSchema: {
+            focus: z.enum(["all", "progress", "contradictions", "gaps", "patterns"]).optional().describe("What aspect to analyze (default: all)"),
+        },
+    }, async (args) => {
+        const history = store.getHistory();
+        if (history.length === 0) {
+            return {
+                content: [{ type: "text", text: JSON.stringify({ summary: "No thoughts to reflect on yet.", patterns: [], suggestions: ["Start thinking first using the 'think' tool."], practiceViolations: [], progress: { totalThoughts: 0, uniqueTopics: 0, branchesExplored: 0, averageConfidence: null, confidenceTrend: "unknown", estimatedCompletion: 0 } }, null, 2) }],
+            };
+        }
+        const focus = args.focus ?? "all";
+        const result = analyzer.analyze(history, store.getBranches(), store.getActiveStrategy(), focus);
+        return {
+            content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+        };
+    });
+}
+//# sourceMappingURL=reflect.js.map

package/server/dist/tools/reflect.js.map

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package/server/dist/tools/strategize.d.ts

@@ -0,0 +1,5 @@
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { ThoughtStore } from "../engine/thought-store.js";
+import type { DeepThinkConfig } from "../types.js";
+export declare function registerStrategizeTool(server: McpServer, store: ThoughtStore, config: DeepThinkConfig): void;
+//# sourceMappingURL=strategize.d.ts.map

package/server/dist/tools/strategize.d.ts.map

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package/server/dist/tools/strategize.js

@@ -0,0 +1,80 @@
+import { z } from "zod";
+import { BUILT_IN_STRATEGIES } from "../engine/strategies.js";
+export function registerStrategizeTool(server, store, config) {
+    server.registerTool("strategize", {
+        title: "Strategize",
+        description: `Switch reasoning frameworks to guide your thinking process. Different problems benefit from different thinking strategies.
+
+Built-in strategies:
+- first-principles: Decompose assumptions and rebuild from ground truth
+- red-team: Attack your own conclusions to find weaknesses
+- convergent: Narrow from many options to one decision
+- divergent: Generate ideas freely without judgment
+- root-cause: Systematic investigation (5 whys, elimination)
+- decision-matrix: Weighted criteria comparison
+
+Custom strategies from .deep-think.json are also available if configured.
+
+Operations:
+- set: Activate a strategy (influences think feedback and reflect analysis)
+- get: Show the current active strategy with its guidance
+- list: Show all available strategies`,
+        inputSchema: {
+            operation: z.enum(["set", "get", "list"]).describe("Strategy operation"),
+            strategy: z.string().optional().describe("Strategy name (for set)"),
+        },
+    }, async (args) => {
+        const allStrategies = getAllStrategies(config);
+        switch (args.operation) {
+            case "list": {
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ strategies: allStrategies.map(s => ({ name: s.name, description: s.description, whenToUse: s.whenToUse })) }, null, 2) }],
+                };
+            }
+            case "get": {
+                const active = store.getActiveStrategy();
+                if (!active) {
+                    return {
+                        content: [{ type: "text", text: JSON.stringify({ activeStrategy: null, message: "No strategy active. Use 'set' to activate one." }, null, 2) }],
+                    };
+                }
+                const strategy = allStrategies.find(s => s.name === active);
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ activeStrategy: strategy ?? { name: active, description: "Unknown strategy" } }, null, 2) }],
+                };
+            }
+            case "set": {
+                if (!args.strategy) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: "set requires a strategy name" }],
+                    };
+                }
+                const exists = allStrategies.some(s => s.name === args.strategy);
+                if (!exists) {
+                    return {
+                        isError: true,
+                        content: [{ type: "text", text: `Unknown strategy: ${args.strategy}. Use 'list' to see available strategies.` }],
+                    };
+                }
+                store.setActiveStrategy(args.strategy);
+                const strategy = allStrategies.find(s => s.name === args.strategy);
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ activated: args.strategy, steps: strategy?.steps, guidingQuestions: strategy?.guidingQuestions }, null, 2) }],
+                };
+            }
+        }
+    });
+}
+function getAllStrategies(config) {
+    const custom = config.strategies.custom.map(cs => ({
+        name: cs.name,
+        description: cs.description,
+        steps: cs.steps,
+        guidingQuestions: [],
+        reflectChecks: [],
+        whenToUse: cs.description,
+    }));
+    return [...BUILT_IN_STRATEGIES, ...custom];
+}
+//# sourceMappingURL=strategize.js.map

package/server/dist/tools/strategize.js.map

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package/server/dist/tools/think.d.ts

@@ -0,0 +1,6 @@
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { ThoughtStore } from "../engine/thought-store.js";
+import type { DeepThinkConfig } from "../types.js";
+import { FileStore } from "../persistence/file-store.js";
+export declare function registerThinkTool(server: McpServer, store: ThoughtStore, config: DeepThinkConfig, fileStore: FileStore): void;
+//# sourceMappingURL=think.d.ts.map

package/server/dist/tools/think.d.ts.map

@@ -0,0 +1 @@
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