@bis-code/deep-think 1.1.1

package/server/dist/tools/think.js

@@ -0,0 +1,129 @@
+import { z } from "zod";
+export function registerThinkTool(server, store, config, fileStore) {
+    server.registerTool("think", {
+        title: "Think",
+        description: `Record a reasoning step in a structured thought chain. Enhanced replacement for sequential thinking.
+
+This tool helps analyze problems through a flexible, persistent thinking process that adapts and evolves.
+Each thought can build on, question, or revise previous insights as understanding deepens.
+
+When to use:
+- Breaking down complex problems into steps
+- Planning and design with room for revision
+- Analysis that might need course correction
+- Problems where the full scope isn't clear initially
+- Tasks needing persistent context across sessions
+
+Enhanced features beyond sequential thinking:
+- Confidence tracking (0-1) on each thought
+- Semantic tags for cross-thought analysis
+- Assumptions and evidence tracking
+- Strategy-guided thinking
+- Active feedback on reasoning patterns
+
+Parameters:
+- thought: Your current thinking step (analysis, revision, question, realization, hypothesis)
+- nextThoughtNeeded: True if more thinking needed, even past the estimated end
+- thoughtNumber: Current position in sequence (1-indexed)
+- totalThoughts: Current estimate of thoughts needed (adjustable up/down)
+- confidence: How confident you are in this step (0-1, optional)
+- tags: Semantic labels for this thought (optional)
+- assumptions: Explicit assumptions being made (optional)
+- evidence: Supporting evidence or references (optional)
+- isRevision: Whether this revises previous thinking
+- revisesThought: Which thought number is being reconsidered
+- branchFromThought: Branching point thought number
+- branchId: Branch identifier
+- needsMoreThoughts: Signal to extend beyond totalThoughts
+
+You should:
+1. Start with an initial estimate of thoughts needed, but adjust freely
+2. Track confidence — it helps the reflect tool detect issues
+3. Tag thoughts for better cross-thought analysis
+4. Make assumptions explicit — they're checked during reflection
+5. Only set nextThoughtNeeded to false when truly satisfied`,
+        inputSchema: {
+            thought: z.string().describe("Your current thinking step"),
+            nextThoughtNeeded: z.boolean().describe("Whether another thought step is needed"),
+            thoughtNumber: z.number().int().min(1).describe("Current thought number"),
+            totalThoughts: z.number().int().min(1).describe("Estimated total thoughts needed"),
+            confidence: z.number().min(0).max(1).optional().describe("Confidence in this step (0-1)"),
+            tags: z.array(z.string()).optional().describe("Semantic tags for this thought"),
+            assumptions: z.array(z.string()).optional().describe("Assumptions being made"),
+            evidence: z.array(z.string()).optional().describe("Supporting evidence"),
+            isRevision: z.boolean().optional().describe("Whether this revises previous thinking"),
+            revisesThought: z.number().int().min(1).optional().describe("Which thought is being reconsidered"),
+            branchFromThought: z.number().int().min(1).optional().describe("Branching point thought number"),
+            branchId: z.string().optional().describe("Branch identifier"),
+            needsMoreThoughts: z.boolean().optional().describe("If more thoughts are needed beyond estimate"),
+            strategy: z.string().optional().describe("Reasoning strategy to apply"),
+            dependsOn: z.array(z.number().int().min(1)).optional().describe("Thought numbers this depends on"),
+        },
+        outputSchema: {
+            thoughtNumber: z.number(),
+            totalThoughts: z.number(),
+            nextThoughtNeeded: z.boolean(),
+            branches: z.array(z.string()),
+            thoughtHistoryLength: z.number(),
+            activeStrategy: z.string().nullable(),
+            feedback: z.array(z.string()),
+        },
+    }, async (args) => {
+        if (args.strategy) {
+            store.setActiveStrategy(args.strategy);
+        }
+        const stored = store.addThought(args);
+        const history = store.getHistory();
+        const feedback = [];
+        // Feedback: chain length warning
+        if (history.length > config.thinking.maxThoughts * 0.8) {
+            feedback.push(`Approaching thought limit (${history.length}/${config.thinking.maxThoughts}). Consider reflecting or concluding.`);
+        }
+        // Feedback: confidence dropping
+        if (history.length >= 3) {
+            const recent = history.slice(-3);
+            const confidences = recent.map(t => t.confidence).filter((c) => c !== undefined);
+            if (confidences.length >= 2) {
+                const trend = confidences[confidences.length - 1] - confidences[0];
+                if (trend < -0.3) {
+                    feedback.push("Confidence has dropped significantly in recent thoughts. Consider using 'reflect' to analyze the chain.");
+                }
+            }
+        }
+        // Feedback: no tags being used
+        if (history.length >= 5 && history.every(t => !t.tags || t.tags.length === 0)) {
+            feedback.push("Tip: Adding tags to thoughts improves the quality of 'reflect' analysis.");
+        }
+        // Auto-checkpoint every N thoughts
+        const autoEvery = config.thinking.autoCheckpointEvery;
+        if (autoEvery > 0 && history.length > 0 && history.length % autoEvery === 0) {
+            const state = store.serialize();
+            const cpName = `auto-${Date.now()}`;
+            await fileStore.save(cpName, {
+                name: cpName,
+                timestamp: new Date().toISOString(),
+                sessionId: store.getSessionId(),
+                thoughtHistory: state.thoughtHistory,
+                branches: state.branches,
+                activeStrategy: state.activeStrategy,
+                metadata: {},
+                projectPath: process.cwd(),
+            });
+            feedback.push(`Auto-checkpoint saved: ${cpName} (every ${autoEvery} thoughts)`);
+        }
+        const response = {
+            thoughtNumber: stored.thoughtNumber,
+            totalThoughts: stored.totalThoughts,
+            nextThoughtNeeded: stored.nextThoughtNeeded,
+            branches: store.getBranchIds(),
+            thoughtHistoryLength: history.length,
+            activeStrategy: store.getActiveStrategy(),
+            feedback,
+        };
+        return {
+            content: [{ type: "text", text: JSON.stringify(response, null, 2) }],
+            structuredContent: response,
+        };
+    });
+}
+//# sourceMappingURL=think.js.map

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

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package/server/dist/types.d.ts

@@ -0,0 +1,148 @@
+export interface ThoughtData {
+    thought: string;
+    thoughtNumber: number;
+    totalThoughts: number;
+    nextThoughtNeeded: boolean;
+    isRevision?: boolean;
+    revisesThought?: number;
+    branchFromThought?: number;
+    branchId?: string;
+    needsMoreThoughts?: boolean;
+    strategy?: string;
+    confidence?: number;
+    tags?: string[];
+    dependsOn?: number[];
+    assumptions?: string[];
+    evidence?: string[];
+}
+export interface StoredThought extends ThoughtData {
+    timestamp: string;
+    sessionId: string;
+}
+export interface ThinkResponse {
+    thoughtNumber: number;
+    totalThoughts: number;
+    nextThoughtNeeded: boolean;
+    branches: string[];
+    thoughtHistoryLength: number;
+    activeStrategy: string | null;
+    feedback: string[];
+}
+export interface ReflectionResult {
+    summary: string;
+    patterns: DetectedPattern[];
+    suggestions: string[];
+    practiceViolations: PracticeViolation[];
+    progress: ProgressSummary;
+}
+export interface DetectedPattern {
+    type: 'circular' | 'contradiction' | 'anchoring' | 'scope-creep' | 'diminishing';
+    description: string;
+    involvedThoughts: number[];
+    severity: 'info' | 'warning' | 'critical';
+}
+export interface PracticeViolation {
+    rule: string;
+    thoughtNumber: number;
+    explanation: string;
+}
+export interface ProgressSummary {
+    totalThoughts: number;
+    uniqueTopics: number;
+    branchesExplored: number;
+    averageConfidence: number | null;
+    confidenceTrend: 'rising' | 'falling' | 'stable' | 'unknown';
+    estimatedCompletion: number;
+}
+export interface BranchInfo {
+    id: string;
+    fromThought: number;
+    thoughtCount: number;
+    summary: string;
+}
+export interface BranchComparison {
+    branchA: string;
+    branchB: string;
+    agreements: string[];
+    disagreements: string[];
+    uniqueToA: string[];
+    uniqueToB: string[];
+}
+export interface MergeResult {
+    mergedFrom: string[];
+    conclusion: string;
+    winningBranch: string | null;
+    rationale: string;
+    mergedThoughtNumber: number;
+}
+export interface CheckpointData {
+    name: string;
+    timestamp: string;
+    sessionId: string;
+    thoughtHistory: StoredThought[];
+    branches: Record<string, StoredThought[]>;
+    activeStrategy: string | null;
+    metadata: Record<string, unknown>;
+    projectPath?: string;
+}
+export interface CheckpointInfo {
+    name: string;
+    timestamp: string;
+    thoughtCount: number;
+    branchCount: number;
+    strategy: string | null;
+    projectPath?: string;
+}
+export interface Strategy {
+    name: string;
+    description: string;
+    steps: string[];
+    guidingQuestions: string[];
+    reflectChecks: string[];
+    whenToUse: string;
+}
+export interface DeepThinkConfig {
+    project: ProjectConfig;
+    thinking: ThinkingConfig;
+    practices: PracticesConfig;
+    strategies: StrategiesConfig;
+    reflection: ReflectionConfig;
+    persistence: PersistenceConfig;
+}
+export interface ProjectConfig {
+    name: string;
+    type: string;
+    language: string;
+    description: string;
+}
+export interface ThinkingConfig {
+    defaultStrategy: string | null;
+    maxThoughts: number;
+    autoCheckpointEvery: number;
+    confidenceThreshold: number;
+}
+export interface PracticesConfig {
+    rules: string[];
+    antiPatterns: string[];
+    reviewChecklist: string[];
+}
+export interface StrategiesConfig {
+    custom: CustomStrategy[];
+}
+export interface CustomStrategy {
+    name: string;
+    description: string;
+    steps: string[];
+    checkpoints: string[];
+}
+export interface ReflectionConfig {
+    alwaysCheck: string[];
+    circularThreshold: number;
+    contradictionSensitivity: 'low' | 'medium' | 'high';
+}
+export interface PersistenceConfig {
+    directory: string;
+    maxCheckpoints: number;
+    autoSave: boolean;
+}
+//# sourceMappingURL=types.d.ts.map

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

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

@@ -0,0 +1,5 @@
+// ============================================================================
+// Core Thought Types
+// ============================================================================
+export {};
+//# sourceMappingURL=types.js.map

package/server/dist/types.js.map

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package/server/package.json

@@ -0,0 +1,36 @@
+{
+  "name": "mcp-deep-think",
+  "version": "1.1.1",
+  "description": "MCP server for structured reasoning — persistent, analytical, strategy-driven thinking",
+  "license": "MIT",
+  "author": "Ioan-Sorin Baicoianu <baicoianuioansorin@gmail.com>",
+  "type": "module",
+  "bin": {
+    "mcp-deep-think": "dist/index.js"
+  },
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "dist"
+  ],
+  "scripts": {
+    "build": "tsc && chmod +x dist/index.js",
+    "bundle": "esbuild src/index.ts --bundle --platform=node --target=node20 --format=esm --outfile=dist/bundle.mjs",
+    "dev": "tsc --watch",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage",
+    "prepublishOnly": "npm run build"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.26.0",
+    "zod": "^3.25.0"
+  },
+  "devDependencies": {
+    "@types/node": "^22",
+    "@vitest/coverage-v8": "^2.1.8",
+    "esbuild": "^0.27.4",
+    "typescript": "^5.3.3",
+    "vitest": "^2.1.8"
+  }
+}

package/skills/manage-constraints/SKILL.md

@@ -0,0 +1,28 @@
+---
+name: manage-constraints
+description: Use when the user conversationally asks to add reasoning rules, constraints, or anti-patterns to their deep-think configuration. Triggers on phrases like "remember to always check X", "add a rule about Y", "from now on check Z during reasoning", "never do X when thinking through problems".
+---
+
+# Manage Deep Think Constraints
+
+The user wants to add, remove, or view constraints that guide deep-think reasoning.
+
+Constraints map to `.deep-think.json` in the current project directory:
+- `practices.rules` — things to always check during reasoning
+- `practices.antiPatterns` — patterns to avoid and flag during reflection
+
+## Steps
+
+1. Read `.deep-think.json` from the current project directory.
+   - If the file doesn't exist, start with an empty config.
+2. Determine what the user wants: add a rule, add an anti-pattern, remove something, or view current constraints.
+3. Make the change to the appropriate array.
+4. Write the updated `.deep-think.json` back to disk.
+5. Confirm what was added/removed/shown.
+
+## Deciding: Rule vs Anti-Pattern
+
+- **Rule**: Something to always check or consider (e.g., "always verify security implications")
+- **Anti-pattern**: Something to avoid and flag if detected (e.g., "premature optimization")
+
+If unclear, ask the user which category fits better.

package/skills/manage-practices/SKILL.md

@@ -0,0 +1,26 @@
+---
+name: manage-practices
+description: Use when the user conversationally asks to add review checklist items, custom reasoning strategies, or modify their deep-think review process. Triggers on phrases like "add a review step for...", "create a strategy for...", "I want to always check for... during review", "add a custom thinking framework".
+---
+
+# Manage Deep Think Practices
+
+The user wants to add, remove, or view review practices and custom strategies.
+
+Practices map to `.deep-think.json` in the current project directory:
+- `practices.reviewChecklist` — items checked during reflection
+- `strategies.custom` — custom reasoning strategies with steps and checkpoints
+
+## Steps
+
+1. Read `.deep-think.json` from the current project directory.
+   - If the file doesn't exist, start with an empty config.
+2. Determine what the user wants: add a review item, add a strategy, remove something, or view current practices.
+3. For review items: add/remove from the `practices.reviewChecklist` array.
+4. For strategies: each custom strategy needs:
+   - `name` — short identifier (kebab-case)
+   - `description` — when to use this strategy
+   - `steps` — ordered list of reasoning steps
+   - `checkpoints` — things to verify at each stage
+5. Write the updated `.deep-think.json` back to disk.
+6. Confirm what was added/removed/shown.

package/skills/restore-checkpoint/SKILL.md

@@ -0,0 +1,25 @@
+---
+name: restore-checkpoint
+description: Use when starting a new session and the user seems to be continuing previous reasoning work, mentions resuming a thought chain, or asks to restore a deep-think checkpoint. Also triggers when a user mentions picking up where they left off on a complex decision or analysis.
+---
+
+# Restore Deep Think Checkpoint
+
+The user may be continuing reasoning work from a previous session.
+
+## Steps
+
+1. Call the deep-think checkpoint tool with operation "list" to see available checkpoints.
+2. If checkpoints exist, present them to the user with name, timestamp, project path, thought count, and strategy.
+3. Ask if they'd like to restore one to continue their reasoning.
+4. If yes, call checkpoint with operation "load" and the chosen name.
+5. After restoring, call reflect with focus "progress" to show where they left off.
+6. Suggest next steps based on the restored state.
+
+## If No Checkpoints
+
+If no checkpoints are found, let the user know and suggest starting fresh with `/deep-think:start`.
+
+## Fallback
+
+If this skill doesn't trigger automatically, users can always run `/deep-think:checkpoints` to manually access the same functionality.