@dragonflymcp/plugin 1.0.0

package/.claude-plugin/plugin.json

@@ -0,0 +1,26 @@
+{
+  "name": "dragonfly",
+  "displayName": "Dragonfly",
+  "description": "Sonnet-optimized MCP plugin: 66 tools for code intelligence, semantic search, memory, and workflow orchestration across 13 modules.",
+  "version": "1.0.0",
+  "author": {
+    "name": "Michael Kolb",
+    "url": "https://github.com/mkolb22"
+  },
+  "homepage": "https://github.com/mkolb22/dragonfly-plugin",
+  "repository": "https://github.com/mkolb22/dragonfly-plugin",
+  "license": "MIT",
+  "categories": [
+    "code-intelligence",
+    "productivity",
+    "workflow"
+  ],
+  "mcpServer": {
+    "command": "node",
+    "args": [
+      "--no-wasm-tier-up",
+      "--liftoff-only",
+      "node_modules/@dragonflymcp/plugin/dist/index.js"
+    ]
+  }
+}

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Michael Kolb
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# Dragonfly
+
+Sonnet-optimized MCP plugin for Claude Code: 66 tools across 13 modules covering code intelligence, semantic search, persistent memory, and workflow orchestration.
+
+## Installation
+
+```bash
+npm install --save-dev @dragonflymcp/plugin
+```
+
+The `postinstall` script runs automatically and deploys all agents, skills, commands, hooks, and `.mcp.json` into your project. Restart Claude Code to activate.
+
+To re-run setup manually at any time:
+
+```bash
+npx dragonfly-init
+```
+
+Setup is idempotent — existing files are never overwritten.
+
+## Modules
+
+| Module | Tools | Description |
+|--------|-------|-------------|
+| AST | 7 | Code intelligence through AST analysis |
+| Semantic | 3 | Semantic search with embeddings |
+| Memory | 4 | Persistent semantic memory |
+| Framework | 8 | Workflow orchestration |
+| State | 8 | Health, checkpoints, stories |
+| Evolve | 4 | Prompt optimization |
+| Spec | 6 | Specification DSL for code generation |
+| Testing | 6 | Test generation, execution, coverage |
+| Repair | 5 | Self-repair and iterative refinement |
+| Knowledge Graph | 7 | Entity/relation management with hybrid search |
+| Analytics | 2 | Cost and performance observability |
+| Pipeline | 2 | Composition DSL and execution planning |
+| Bridge | 4 | Cross-project memory export/import/search |
+
+## What Gets Deployed
+
+| Destination | Count | Source |
+|-------------|-------|--------|
+| `.claude/agents/` | 18 agents | `templates/agents/*.md` |
+| `.claude/skills/` | 43 skills | `templates/skills/*.md.template` |
+| `.claude/commands/` | 31 commands | `templates/commands/*.md.template` |
+| `.claude/hooks/` | 15 hooks + lib | `templates/hooks/*.template` |
+| `.mcp.json` | MCP server config | written by init script |
+
+## Feature Flags
+
+Modules are opt-in via environment variables. Set in your `.mcp.json` `env` block or shell:
+
+```bash
+DRAGONFLY_MEMORY_ENABLED=true
+DRAGONFLY_FRAMEWORK_ENABLED=true
+DRAGONFLY_STATE_ENABLED=true
+DRAGONFLY_EVOLVE_ENABLED=true
+DRAGONFLY_SPEC_ENABLED=true
+DRAGONFLY_REPAIR_ENABLED=true
+DRAGONFLY_KG_ENABLED=true
+DRAGONFLY_ANALYTICS_ENABLED=true
+DRAGONFLY_PIPELINE_ENABLED=true
+DRAGONFLY_BRIDGE_ENABLED=true
+```
+
+AST, Semantic, and Testing modules are always enabled.
+
+## Environment Variables
+
+```bash
+PROJECT_ROOT                      # working directory (default: cwd)
+DRAGONFLY_STATE_DB_PATH           # override state DB path
+DRAGONFLY_MEMORY_DB_PATH          # override memory DB path
+DRAGONFLY_INDEX_PATH              # override AST index path
+DRAGONFLY_FRAMEWORK_CONTENT_ROOT  # override templates path
+DRAGONFLY_DEBUG=true              # enable debug logging
+```
+
+## Data Directory
+
+Dragonfly stores all runtime state in `data/` at the project root:
+
+```
+data/
+├── index/       # AST index (rebuilt via index_project tool)
+├── state.db     # checkpoints, stories, workflows, specs
+└── memory.db    # memories, embeddings, knowledge graph
+```
+
+Add `data/` to `.gitignore`. It is created automatically on first run.
+
+## MCP Configuration
+
+The init script writes this to `.mcp.json`:
+
+```json
+{
+  "mcpServers": {
+    "dragonfly": {
+      "type": "stdio",
+      "command": "node",
+      "args": [
+        "--no-wasm-tier-up",
+        "--liftoff-only",
+        "node_modules/@dragonflymcp/plugin/dist/index.js"
+      ]
+    }
+  }
+}
+```
+
+The WASM flags are required for tree-sitter stability.
+
+## Building from Source
+
+```bash
+git clone https://github.com/mkolb22/dragonfly-plugin
+cd dragonfly-plugin
+npm install
+npm run build    # tsc — must be 0 errors
+npm run test:run # vitest run
+```
+
+## License
+
+MIT

package/dist/core/annotations.d.ts

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+/**
+ * Tool Annotations
+ * Safety metadata for intelligent tool routing and execution
+ */
+/**
+ * Tool execution safety levels
+ */
+export declare enum ToolSafety {
+    /** Read-only data access (idempotent, no side effects) */
+    ReadOnly = "read_only",
+    /** Read-only but accesses external systems (network, filesystem) */
+    ReadOnlyExternal = "read_only_external",
+    /** Creates or modifies data (non-idempotent) */
+    Mutating = "mutating",
+    /** Modifies data but safe to retry (idempotent mutation) */
+    IdempotentMutation = "idempotent_mutation",
+    /** Deletes or archives data (requires careful handling) */
+    Destructive = "destructive"
+}
+/**
+ * Tool annotation metadata
+ */
+export interface ToolAnnotation {
+    /** Safety level for execution decisions */
+    safety: ToolSafety;
+    /** Human-readable title for UI/logging */
+    title: string;
+    /** Estimated cost tier (for routing decisions) */
+    costTier?: "low" | "medium" | "high";
+    /** Whether tool requires confirmation in cautious mode */
+    requiresConfirmation?: boolean;
+    /** Tags for categorization */
+    tags?: string[];
+}
+/**
+ * Create a tool annotation
+ */
+export declare function annotate(safety: ToolSafety, title: string, options?: Partial<Omit<ToolAnnotation, "safety" | "title">>): ToolAnnotation;
+/**
+ * Pre-built annotation helpers
+ */
+export declare const Annotations: {
+    /** Read-only tool that queries data */
+    readOnly: (title: string, tags?: string[]) => ToolAnnotation;
+    /** Read-only but accesses external resources */
+    readOnlyExternal: (title: string, tags?: string[]) => ToolAnnotation;
+    /** Tool that creates or modifies data */
+    mutating: (title: string, tags?: string[]) => ToolAnnotation;
+    /** Safe-to-retry mutation */
+    idempotent: (title: string, tags?: string[]) => ToolAnnotation;
+    /** Destructive operation requiring confirmation */
+    destructive: (title: string, tags?: string[]) => ToolAnnotation;
+};
+/**
+ * Tool definition with annotation
+ */
+export interface AnnotatedTool {
+    name: string;
+    description: string;
+    inputSchema: object;
+    annotation: ToolAnnotation;
+}
+/**
+ * Check if a tool is safe to execute without confirmation
+ */
+export declare function isSafeToExecute(annotation: ToolAnnotation): boolean;
+/**
+ * Get tools filtered by safety level
+ */
+export declare function filterBySafety(tools: AnnotatedTool[], safety: ToolSafety | ToolSafety[]): AnnotatedTool[];
+//# sourceMappingURL=annotations.d.ts.map

package/dist/core/annotations.d.ts.map

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package/dist/core/annotations.js

@@ -0,0 +1,61 @@
+/**
+ * Tool Annotations
+ * Safety metadata for intelligent tool routing and execution
+ */
+/**
+ * Tool execution safety levels
+ */
+export var ToolSafety;
+(function (ToolSafety) {
+    /** Read-only data access (idempotent, no side effects) */
+    ToolSafety["ReadOnly"] = "read_only";
+    /** Read-only but accesses external systems (network, filesystem) */
+    ToolSafety["ReadOnlyExternal"] = "read_only_external";
+    /** Creates or modifies data (non-idempotent) */
+    ToolSafety["Mutating"] = "mutating";
+    /** Modifies data but safe to retry (idempotent mutation) */
+    ToolSafety["IdempotentMutation"] = "idempotent_mutation";
+    /** Deletes or archives data (requires careful handling) */
+    ToolSafety["Destructive"] = "destructive";
+})(ToolSafety || (ToolSafety = {}));
+/**
+ * Create a tool annotation
+ */
+export function annotate(safety, title, options) {
+    return {
+        safety,
+        title,
+        ...options,
+    };
+}
+/**
+ * Pre-built annotation helpers
+ */
+export const Annotations = {
+    /** Read-only tool that queries data */
+    readOnly: (title, tags) => annotate(ToolSafety.ReadOnly, title, { costTier: "low", tags }),
+    /** Read-only but accesses external resources */
+    readOnlyExternal: (title, tags) => annotate(ToolSafety.ReadOnlyExternal, title, { costTier: "medium", tags }),
+    /** Tool that creates or modifies data */
+    mutating: (title, tags) => annotate(ToolSafety.Mutating, title, { costTier: "medium", requiresConfirmation: true, tags }),
+    /** Safe-to-retry mutation */
+    idempotent: (title, tags) => annotate(ToolSafety.IdempotentMutation, title, { costTier: "medium", tags }),
+    /** Destructive operation requiring confirmation */
+    destructive: (title, tags) => annotate(ToolSafety.Destructive, title, { costTier: "high", requiresConfirmation: true, tags }),
+};
+/**
+ * Check if a tool is safe to execute without confirmation
+ */
+export function isSafeToExecute(annotation) {
+    return (annotation.safety === ToolSafety.ReadOnly ||
+        annotation.safety === ToolSafety.ReadOnlyExternal ||
+        annotation.safety === ToolSafety.IdempotentMutation);
+}
+/**
+ * Get tools filtered by safety level
+ */
+export function filterBySafety(tools, safety) {
+    const safetyLevels = Array.isArray(safety) ? safety : [safety];
+    return tools.filter((t) => safetyLevels.includes(t.annotation.safety));
+}
+//# sourceMappingURL=annotations.js.map

package/dist/core/annotations.js.map

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package/dist/core/config.d.ts

@@ -0,0 +1,66 @@
+/**
+ * Configuration Management
+ * Centralized, type-safe configuration with environment variable support
+ */
+/**
+ * Server configuration
+ */
+export interface DragonflyConfig {
+    serverName: string;
+    serverVersion: string;
+    projectRoot: string;
+    indexPath: string;
+    astMaxFileSize: number;
+    astExcludePatterns: string[];
+    astIncrementalDefault: boolean;
+    embeddingModel: string;
+    embeddingDimensions: number;
+    semanticChunkSize: number;
+    semanticChunkOverlap: number;
+    semanticMaxResults: number;
+    semanticMinSimilarity: number;
+    memoryEnabled: boolean;
+    memoryDbPath: string;
+    memoryDecayGraceDays: number;
+    memoryDecayBaseRate: number;
+    memoryDecayThreshold: number;
+    memoryAutoLinkThreshold: number;
+    frameworkEnabled: boolean;
+    frameworkContentRoot: string;
+    stateEnabled: boolean;
+    stateDbPath: string;
+    evolveEnabled: boolean;
+    specEnabled: boolean;
+    repairEnabled: boolean;
+    repairMaxIterations: number;
+    repairTimeout: number;
+    repairHistoryLimit: number;
+    kgEnabled: boolean;
+    kgSemanticWeight: number;
+    kgKeywordWeight: number;
+    kgGraphWeight: number;
+    kgCommunityWeight: number;
+    analyticsEnabled: boolean;
+    pipelineEnabled: boolean;
+    bridgeEnabled: boolean;
+    bridgeGlobalMemoryPath: string;
+    debugMode: boolean;
+    verboseLogging: boolean;
+}
+/**
+ * Default configuration with environment overrides
+ */
+export declare function getConfig(): DragonflyConfig;
+/**
+ * Get or create config instance
+ */
+export declare const config: () => DragonflyConfig;
+/**
+ * Reset config (for testing)
+ */
+export declare const resetConfig: () => void;
+/**
+ * Log config summary (for debugging)
+ */
+export declare function logConfig(cfg?: DragonflyConfig): void;
+//# sourceMappingURL=config.d.ts.map

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package/dist/core/config.js

@@ -0,0 +1,131 @@
+/**
+ * Configuration Management
+ * Centralized, type-safe configuration with environment variable support
+ */
+/**
+ * Environment variable helpers
+ */
+function envOr(key, defaultValue) {
+    return process.env[key] || defaultValue;
+}
+function envInt(key, defaultValue) {
+    const value = process.env[key];
+    if (!value)
+        return defaultValue;
+    const parsed = parseInt(value, 10);
+    return isNaN(parsed) ? defaultValue : parsed;
+}
+function envFloat(key, defaultValue) {
+    const value = process.env[key];
+    if (!value)
+        return defaultValue;
+    const parsed = parseFloat(value);
+    return isNaN(parsed) ? defaultValue : parsed;
+}
+function envBool(key, defaultValue) {
+    const value = process.env[key]?.toLowerCase();
+    if (!value)
+        return defaultValue;
+    return value === "true" || value === "1" || value === "yes";
+}
+function envArray(key, defaultValue) {
+    const value = process.env[key];
+    if (!value)
+        return defaultValue;
+    return value.split(",").map((s) => s.trim()).filter(Boolean);
+}
+/**
+ * Default configuration with environment overrides
+ */
+export function getConfig() {
+    const projectRoot = envOr("PROJECT_ROOT", process.cwd());
+    return {
+        // Server
+        serverName: envOr("DRAGONFLY_SERVER_NAME", "dragonfly-server"),
+        serverVersion: envOr("DRAGONFLY_SERVER_VERSION", "1.0.0"),
+        // Paths
+        projectRoot,
+        indexPath: envOr("DRAGONFLY_INDEX_PATH", `${projectRoot}/data/index`),
+        // AST Indexing
+        astMaxFileSize: envInt("DRAGONFLY_AST_MAX_FILE_SIZE", 1024 * 1024), // 1MB
+        astExcludePatterns: envArray("DRAGONFLY_AST_EXCLUDE", [
+            "node_modules",
+            ".git",
+            "dist",
+            "build",
+            "__pycache__",
+            ".pytest_cache",
+            "coverage",
+        ]),
+        astIncrementalDefault: envBool("DRAGONFLY_AST_INCREMENTAL", true),
+        // Semantic Search
+        embeddingModel: envOr("DRAGONFLY_EMBEDDING_MODEL", "all-MiniLM-L6-v2"),
+        embeddingDimensions: envInt("DRAGONFLY_EMBEDDING_DIMS", 384),
+        semanticChunkSize: envInt("DRAGONFLY_CHUNK_SIZE", 512),
+        semanticChunkOverlap: envInt("DRAGONFLY_CHUNK_OVERLAP", 50),
+        semanticMaxResults: envInt("DRAGONFLY_MAX_RESULTS", 10),
+        semanticMinSimilarity: envFloat("DRAGONFLY_MIN_SIMILARITY", 0.3),
+        // Memory System
+        memoryEnabled: envBool("DRAGONFLY_MEMORY_ENABLED", true),
+        memoryDbPath: envOr("DRAGONFLY_MEMORY_DB_PATH", `${projectRoot}/data/memory.db`),
+        memoryDecayGraceDays: envInt("DRAGONFLY_MEMORY_DECAY_GRACE_DAYS", 7),
+        memoryDecayBaseRate: envFloat("DRAGONFLY_MEMORY_DECAY_BASE_RATE", 0.05),
+        memoryDecayThreshold: envFloat("DRAGONFLY_MEMORY_DECAY_THRESHOLD", 0.1),
+        memoryAutoLinkThreshold: envFloat("DRAGONFLY_MEMORY_AUTO_LINK_THRESHOLD", 0.3),
+        // Framework — templates/ is bundled in this repository
+        frameworkEnabled: envBool("DRAGONFLY_FRAMEWORK_ENABLED", true),
+        frameworkContentRoot: envOr("DRAGONFLY_FRAMEWORK_CONTENT_ROOT", `${projectRoot}/templates`),
+        // State Store
+        stateEnabled: envBool("DRAGONFLY_STATE_ENABLED", true),
+        stateDbPath: envOr("DRAGONFLY_STATE_DB_PATH", `${projectRoot}/data/state.db`),
+        // Evolution
+        evolveEnabled: envBool("DRAGONFLY_EVOLVE_ENABLED", true),
+        // Spec
+        specEnabled: envBool("DRAGONFLY_SPEC_ENABLED", true),
+        // Repair
+        repairEnabled: envBool("DRAGONFLY_REPAIR_ENABLED", true),
+        repairMaxIterations: envInt("DRAGONFLY_REPAIR_MAX_ITER", 5),
+        repairTimeout: envInt("DRAGONFLY_REPAIR_TIMEOUT", 120000),
+        repairHistoryLimit: envInt("DRAGONFLY_REPAIR_HISTORY", 100),
+        // Knowledge Graph
+        kgEnabled: envBool("DRAGONFLY_KG_ENABLED", true),
+        kgSemanticWeight: envFloat("DRAGONFLY_KG_SEMANTIC_WEIGHT", 0.4),
+        kgKeywordWeight: envFloat("DRAGONFLY_KG_KEYWORD_WEIGHT", 0.3),
+        kgGraphWeight: envFloat("DRAGONFLY_KG_GRAPH_WEIGHT", 0.2),
+        kgCommunityWeight: envFloat("DRAGONFLY_KG_COMMUNITY_WEIGHT", 0.1),
+        // Analytics
+        analyticsEnabled: envBool("DRAGONFLY_ANALYTICS_ENABLED", true),
+        // Pipeline
+        pipelineEnabled: envBool("DRAGONFLY_PIPELINE_ENABLED", true),
+        // Bridge
+        bridgeEnabled: envBool("DRAGONFLY_BRIDGE_ENABLED", true),
+        bridgeGlobalMemoryPath: envOr("DRAGONFLY_BRIDGE_GLOBAL_MEMORY_PATH", `${process.env.HOME || "/tmp"}/.dragonfly/global-memory`),
+        // Feature Flags
+        debugMode: envBool("DRAGONFLY_DEBUG", false),
+        verboseLogging: envBool("DRAGONFLY_VERBOSE", false),
+    };
+}
+import { createResettableLazyLoader } from "../utils/lazy.js";
+const configLoader = createResettableLazyLoader(() => getConfig());
+/**
+ * Get or create config instance
+ */
+export const config = configLoader.get;
+/**
+ * Reset config (for testing)
+ */
+export const resetConfig = configLoader.reset;
+/**
+ * Log config summary (for debugging)
+ */
+export function logConfig(cfg = config()) {
+    console.error(`[dragonfly] Configuration:`);
+    console.error(`  Server: ${cfg.serverName} v${cfg.serverVersion}`);
+    console.error(`  Project: ${cfg.projectRoot}`);
+    console.error(`  Index: ${cfg.indexPath}`);
+    console.error(`  State: ${cfg.stateDbPath}`);
+    console.error(`  Memory: ${cfg.memoryDbPath}`);
+    console.error(`  Features:`);
+    console.error(`    - Debug: ${cfg.debugMode}`);
+}
+//# sourceMappingURL=config.js.map

package/dist/core/config.js.map

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package/dist/core/dispatcher.d.ts

@@ -0,0 +1,77 @@
+/**
+ * Tool Dispatcher
+ * Centralized tool routing with timeout wrappers and fluent registration
+ */
+import type { Tool } from "@modelcontextprotocol/sdk/types.js";
+import type { ToolModule, ToolResponse } from "./types.js";
+import type { ToolAnnotation } from "./annotations.js";
+/**
+ * Handler function type
+ */
+export type HandlerFn = (args: Record<string, unknown>) => Promise<ToolResponse>;
+/**
+ * Default timeouts
+ */
+export declare const Timeouts: {
+    quick: number;
+    default: number;
+    long: number;
+    veryLong: number;
+};
+/**
+ * Tool Dispatcher
+ * Manages tool registration and dispatch with fluent API
+ */
+export declare class Dispatcher {
+    private handlers;
+    /**
+     * Register a handler with default timeout
+     */
+    register(name: string, fn: HandlerFn, annotation?: ToolAnnotation): this;
+    /**
+     * Register with quick timeout (5s)
+     */
+    registerQuick(name: string, fn: HandlerFn, annotation?: ToolAnnotation): this;
+    /**
+     * Register with long timeout (2min)
+     */
+    registerLong(name: string, fn: HandlerFn, annotation?: ToolAnnotation): this;
+    /**
+     * Register with very long timeout (5min)
+     */
+    registerVeryLong(name: string, fn: HandlerFn, annotation?: ToolAnnotation): this;
+    /**
+     * Register with custom timeout
+     */
+    registerWithTimeout(name: string, fn: HandlerFn, timeout: number, annotation?: ToolAnnotation): this;
+    /**
+     * Dispatch a tool call
+     */
+    dispatch(name: string, args: Record<string, unknown>): Promise<ToolResponse>;
+    /**
+     * Check if a tool is registered
+     */
+    has(name: string): boolean;
+    /**
+     * Get all registered tool names
+     */
+    names(): string[];
+    /**
+     * Get annotation for a tool
+     */
+    getAnnotation(name: string): ToolAnnotation | undefined;
+    /**
+     * Get handler count
+     */
+    get size(): number;
+}
+/**
+ * Create a new dispatcher
+ */
+export declare function createDispatcher(): Dispatcher;
+/**
+ * Create a standard module export from tools array and dispatcher.
+ * Replaces the repeated handleToolCall + module export boilerplate.
+ */
+export declare function createModule(tools: Tool[], dispatcher: Dispatcher): ToolModule;
+//# sourceMappingURL=dispatcher.d.ts.map

package/dist/core/dispatcher.d.ts.map

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