gnosys-mcp 0.1.0

package/dist/lib/ingest.js

@@ -0,0 +1,134 @@
+/**
+ * Gnosys Smart Ingestion — Uses LLM to structure raw input into atomic memories.
+ * Accepts messy human input, produces clean markdown files with YAML frontmatter.
+ */
+import Anthropic from "@anthropic-ai/sdk";
+export class GnosysIngestion {
+    client = null;
+    tagRegistry;
+    store;
+    constructor(store, tagRegistry) {
+        this.store = store;
+        this.tagRegistry = tagRegistry;
+        // Initialize Anthropic client if API key is available
+        const apiKey = process.env.ANTHROPIC_API_KEY;
+        if (apiKey) {
+            this.client = new Anthropic({ apiKey });
+        }
+    }
+    get isLLMAvailable() {
+        return this.client !== null;
+    }
+    /**
+     * Ingest raw text and structure it into an atomic memory.
+     * Uses LLM if available, otherwise requires structured input.
+     */
+    async ingest(rawInput) {
+        if (!this.client) {
+            throw new Error("No ANTHROPIC_API_KEY set. Smart ingestion requires an LLM. " +
+                "Set the ANTHROPIC_API_KEY environment variable or use gnosys_add_structured.");
+        }
+        const registry = this.tagRegistry.getRegistry();
+        const categories = await this.store.getCategories();
+        const systemPrompt = `You are Gnosys, a knowledge management system. Your job is to take raw, unstructured input and produce a structured atomic memory.
+
+An atomic memory is ONE concept, decision, or piece of knowledge per file. If the input contains multiple concepts, focus on the primary one.
+
+You must output valid JSON with these fields:
+- title: A clear, concise title for this memory
+- category: One of the existing categories or suggest a new one. Existing: ${categories.join(", ")}
+- tags: An object with tag categories as keys and arrays of tags as values. Use ONLY tags from the registry below. If no existing tag fits, include a "proposed_new_tags" array.
+- relevance: A keyword cloud (space-separated words, NOT sentences) describing every context where this memory would be useful. Include synonyms, related terms, abbreviations, and domain variations. Example: "auth authentication OAuth JWT login session tokens SSO identity credentials access-control permissions RBAC". Be generous — 15-30 keywords. This field powers discovery search.
+- content: The memory content as clean markdown prose (NOT including the title as an H1 — that's added automatically)
+- confidence: 0.0 to 1.0 — how confident you are this is a well-formed atomic memory
+- filename: A kebab-case filename (without .md extension)
+
+TAG REGISTRY:
+${Object.entries(registry)
+            .map(([cat, tags]) => `${cat}: ${tags.join(", ")}`)
+            .join("\n")}
+
+Rules:
+1. One concept per memory. If the input is about multiple things, pick the most important one.
+2. Use existing tags from the registry. Only propose new tags if nothing fits.
+3. The content should be self-contained — someone reading just this file should understand the concept.
+4. Be concise. Memories are meant to be quickly scanned, not deeply read.
+5. Write in third person or neutral voice, not first person.
+6. The relevance field is critical for discovery. Include all terms an agent might use to find this memory — think about what someone working on a related task would search for.`;
+        const response = await this.client.messages.create({
+            model: "claude-haiku-4-5-20251001",
+            max_tokens: 2000,
+            system: systemPrompt,
+            messages: [
+                {
+                    role: "user",
+                    content: `Structure this into an atomic memory:\n\n${rawInput}`,
+                },
+            ],
+        });
+        // Extract text from response
+        const text = response.content[0].type === "text" ? response.content[0].text : "";
+        // Parse JSON from response (handle markdown code blocks)
+        const jsonMatch = text.match(/```json\s*([\s\S]*?)```/) ||
+            text.match(/```\s*([\s\S]*?)```/) || [null, text];
+        const parsed = JSON.parse(jsonMatch[1] || text);
+        // Validate and clean up tags
+        const cleanTags = {};
+        const proposedNewTags = [];
+        if (parsed.tags && typeof parsed.tags === "object") {
+            for (const [cat, tags] of Object.entries(parsed.tags)) {
+                if (Array.isArray(tags)) {
+                    const validTags = [];
+                    for (const tag of tags) {
+                        if (this.tagRegistry.hasTag(tag)) {
+                            validTags.push(tag);
+                        }
+                        else {
+                            proposedNewTags.push({ category: cat, tag });
+                        }
+                    }
+                    if (validTags.length > 0)
+                        cleanTags[cat] = validTags;
+                }
+            }
+        }
+        // Add any explicitly proposed new tags
+        if (parsed.proposed_new_tags) {
+            for (const item of parsed.proposed_new_tags) {
+                proposedNewTags.push(item);
+            }
+        }
+        return {
+            title: parsed.title || "Untitled Memory",
+            category: parsed.category || "uncategorized",
+            tags: cleanTags,
+            relevance: parsed.relevance || "",
+            content: parsed.content || rawInput,
+            confidence: parsed.confidence || 0.7,
+            filename: parsed.filename || this.slugify(parsed.title || "memory"),
+            proposedNewTags: proposedNewTags.length > 0 ? proposedNewTags : undefined,
+        };
+    }
+    /**
+     * Create a memory from already-structured input (no LLM needed).
+     */
+    createStructured(input) {
+        return {
+            title: input.title,
+            category: input.category,
+            tags: input.tags,
+            relevance: input.relevance || "",
+            content: input.content,
+            confidence: input.confidence || 0.8,
+            filename: this.slugify(input.title),
+        };
+    }
+    slugify(text) {
+        return text
+            .toLowerCase()
+            .replace(/[^a-z0-9]+/g, "-")
+            .replace(/^-|-$/g, "")
+            .substring(0, 60);
+    }
+}
+//# sourceMappingURL=ingest.js.map

package/dist/lib/ingest.js.map

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package/dist/lib/lensing.d.ts

@@ -0,0 +1,35 @@
+/**
+ * Gnosys Lensing — Filtered views of the memory store.
+ *
+ * A lens is a set of filter criteria applied to memories.
+ * Compound lenses combine multiple filters with AND/OR logic.
+ */
+import { Memory } from "./store.js";
+export interface LensFilter {
+    category?: string;
+    tags?: string[];
+    tagMatchMode?: "any" | "all";
+    status?: ("active" | "archived" | "superseded")[];
+    author?: ("human" | "ai" | "human+ai")[];
+    authority?: ("declared" | "observed" | "imported" | "inferred")[];
+    minConfidence?: number;
+    maxConfidence?: number;
+    createdAfter?: string;
+    createdBefore?: string;
+    modifiedAfter?: string;
+    modifiedBefore?: string;
+}
+export type CompoundOperator = "AND" | "OR";
+export interface CompoundLens {
+    filters: LensFilter[];
+    operator: CompoundOperator;
+}
+/**
+ * Apply a single lens filter to an array of memories.
+ */
+export declare function applyLens(memories: Memory[], lens: LensFilter): Memory[];
+/**
+ * Apply a compound lens (multiple filters combined with AND/OR).
+ */
+export declare function applyCompoundLens(memories: Memory[], compound: CompoundLens): Memory[];
+//# sourceMappingURL=lensing.d.ts.map

package/dist/lib/lensing.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/lensing.js

@@ -0,0 +1,85 @@
+/**
+ * Gnosys Lensing — Filtered views of the memory store.
+ *
+ * A lens is a set of filter criteria applied to memories.
+ * Compound lenses combine multiple filters with AND/OR logic.
+ */
+/**
+ * Apply a single lens filter to an array of memories.
+ */
+export function applyLens(memories, lens) {
+    return memories.filter((m) => matchesLens(m, lens));
+}
+/**
+ * Apply a compound lens (multiple filters combined with AND/OR).
+ */
+export function applyCompoundLens(memories, compound) {
+    if (compound.filters.length === 0)
+        return memories;
+    if (compound.operator === "AND") {
+        // AND: memory must match ALL filters
+        return memories.filter((m) => compound.filters.every((f) => matchesLens(m, f)));
+    }
+    else {
+        // OR: memory must match ANY filter
+        return memories.filter((m) => compound.filters.some((f) => matchesLens(m, f)));
+    }
+}
+/**
+ * Check if a single memory matches a lens filter.
+ */
+function matchesLens(m, lens) {
+    const fm = m.frontmatter;
+    // Category filter
+    if (lens.category && fm.category !== lens.category)
+        return false;
+    // Status filter (array — memory must match one of the listed statuses)
+    if (lens.status && lens.status.length > 0) {
+        if (!lens.status.includes(fm.status))
+            return false;
+    }
+    // Author filter
+    if (lens.author && lens.author.length > 0) {
+        if (!lens.author.includes(fm.author))
+            return false;
+    }
+    // Authority filter
+    if (lens.authority && lens.authority.length > 0) {
+        if (!lens.authority.includes(fm.authority))
+            return false;
+    }
+    // Confidence range
+    if (lens.minConfidence !== undefined && fm.confidence < lens.minConfidence)
+        return false;
+    if (lens.maxConfidence !== undefined && fm.confidence > lens.maxConfidence)
+        return false;
+    // Tag matching
+    if (lens.tags && lens.tags.length > 0) {
+        const memTags = flattenTags(fm.tags);
+        const mode = lens.tagMatchMode ?? "any";
+        const matches = lens.tags.filter((t) => memTags.includes(t));
+        if (mode === "all" && matches.length !== lens.tags.length)
+            return false;
+        if (mode === "any" && matches.length === 0)
+            return false;
+    }
+    // Date filters
+    if (lens.createdAfter && fm.created < lens.createdAfter)
+        return false;
+    if (lens.createdBefore && fm.created > lens.createdBefore)
+        return false;
+    if (lens.modifiedAfter && fm.modified < lens.modifiedAfter)
+        return false;
+    if (lens.modifiedBefore && fm.modified > lens.modifiedBefore)
+        return false;
+    return true;
+}
+/**
+ * Flatten tags from either format to a simple string array.
+ */
+function flattenTags(tags) {
+    if (Array.isArray(tags))
+        return tags;
+    return Object.values(tags).flat();
+}
+//# sourceMappingURL=lensing.js.map

package/dist/lib/lensing.js.map

@@ -0,0 +1 @@
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package/dist/lib/resolver.d.ts

@@ -0,0 +1,84 @@
+/**
+ * Gnosys Store Resolver — Discovers and manages layered stores.
+ *
+ * Four layers, resolved in specificity order:
+ *   Project  (auto-discovered from cwd, writable, default write target)
+ *   Optional (GNOSYS_STORES, read-only)
+ *   Personal (GNOSYS_PERSONAL, writable, fallback write target)
+ *   Global   (GNOSYS_GLOBAL, writable only when explicitly targeted)
+ */
+import { GnosysStore, Memory } from "./store.js";
+export type StoreLayer = "project" | "personal" | "global" | "optional";
+export interface ResolvedStore {
+    layer: StoreLayer;
+    label: string;
+    store: GnosysStore;
+    writable: boolean;
+    path: string;
+}
+export interface LayeredMemory extends Memory {
+    sourceLayer: StoreLayer;
+    sourceLabel: string;
+}
+export declare class GnosysResolver {
+    private stores;
+    /**
+     * Discover and initialize all store layers.
+     */
+    resolve(): Promise<ResolvedStore[]>;
+    /**
+     * Get all stores in precedence order.
+     */
+    getStores(): ResolvedStore[];
+    /**
+     * Get all memories across all stores, tagged with their source.
+     */
+    getAllMemories(): Promise<LayeredMemory[]>;
+    /**
+     * Read a memory, searching stores in precedence order.
+     * Path format: "layer:category/filename.md" or just "category/filename.md" (searches all).
+     */
+    readMemory(memPath: string): Promise<LayeredMemory | null>;
+    /**
+     * Get the writable store for a given target layer.
+     *
+     * When no target is specified, auto-selects: project → personal.
+     * Global is writable but NEVER auto-selected — it must be explicitly
+     * requested (store: "global"). This prevents accidental writes to
+     * shared org knowledge.
+     * Optional stores are always read-only.
+     */
+    getWriteTarget(target?: StoreLayer): ResolvedStore | null;
+    /**
+     * Get a summary of all active stores for logging.
+     */
+    getSummary(): string;
+    /**
+     * Register a project directory in the persistent project registry.
+     * Called by gnosys_init after creating a new store.
+     */
+    registerProject(projectDir: string): Promise<void>;
+    /**
+     * Directly add a project store to the active stores list.
+     * Used after gnosys_init creates a store, to avoid re-resolving from cwd.
+     */
+    addProjectStore(storePath: string): Promise<void>;
+    /**
+     * Find a project store. Checks registered projects first (from
+     * ~/.config/gnosys/projects.json), then walks up from cwd as fallback.
+     */
+    private findProjectStore;
+    /**
+     * Read registered project directories from persistent config.
+     */
+    private getRegisteredProjects;
+    /**
+     * Path to the persistent project registry file.
+     */
+    private getRegistryPath;
+    /**
+     * Check if a path looks like a valid Gnosys store.
+     */
+    private isValidStore;
+}
+//# sourceMappingURL=resolver.d.ts.map

package/dist/lib/resolver.d.ts.map

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package/dist/lib/resolver.js

@@ -0,0 +1,269 @@
+/**
+ * Gnosys Store Resolver — Discovers and manages layered stores.
+ *
+ * Four layers, resolved in specificity order:
+ *   Project  (auto-discovered from cwd, writable, default write target)
+ *   Optional (GNOSYS_STORES, read-only)
+ *   Personal (GNOSYS_PERSONAL, writable, fallback write target)
+ *   Global   (GNOSYS_GLOBAL, writable only when explicitly targeted)
+ */
+import fs from "fs/promises";
+import path from "path";
+import { GnosysStore } from "./store.js";
+export class GnosysResolver {
+    stores = [];
+    /**
+     * Discover and initialize all store layers.
+     */
+    async resolve() {
+        this.stores = [];
+        // 1. Project store — check registered projects first, then walk up from cwd.
+        //    Registered projects are saved in ~/.config/gnosys/projects.json by gnosys_init.
+        //    This is more reliable than cwd because MCP servers may be spawned
+        //    with cwd set to the user's home directory rather than the open project.
+        const projectPath = await this.findProjectStore();
+        if (projectPath) {
+            const store = new GnosysStore(projectPath);
+            await store.init();
+            this.stores.push({
+                layer: "project",
+                label: "project",
+                store,
+                writable: true,
+                path: projectPath,
+            });
+        }
+        // 2. Optional stores (GNOSYS_STORES — colon-separated)
+        const optionalPaths = process.env.GNOSYS_STORES;
+        if (optionalPaths) {
+            const paths = optionalPaths.split(":").filter(Boolean);
+            for (let i = 0; i < paths.length; i++) {
+                const p = path.resolve(paths[i]);
+                if (await this.isValidStore(p)) {
+                    const store = new GnosysStore(p);
+                    await store.init();
+                    const dirName = path.basename(path.dirname(p)) || path.basename(p);
+                    this.stores.push({
+                        layer: "optional",
+                        label: `optional:${dirName}`,
+                        store,
+                        writable: false,
+                        path: p,
+                    });
+                }
+            }
+        }
+        // 3. Personal store (GNOSYS_PERSONAL)
+        const personalPath = process.env.GNOSYS_PERSONAL;
+        if (personalPath) {
+            const p = path.resolve(personalPath);
+            const store = new GnosysStore(p);
+            await store.init();
+            this.stores.push({
+                layer: "personal",
+                label: "personal",
+                store,
+                writable: true,
+                path: p,
+            });
+        }
+        // 4. Global store (GNOSYS_GLOBAL)
+        //    Writable, but only when explicitly targeted — never auto-selected.
+        const globalPath = process.env.GNOSYS_GLOBAL;
+        if (globalPath) {
+            const p = path.resolve(globalPath);
+            if (await this.isValidStore(p)) {
+                const store = new GnosysStore(p);
+                await store.init();
+                this.stores.push({
+                    layer: "global",
+                    label: "global",
+                    store,
+                    writable: true,
+                    path: p,
+                });
+            }
+        }
+        return this.stores;
+    }
+    /**
+     * Get all stores in precedence order.
+     */
+    getStores() {
+        return this.stores;
+    }
+    /**
+     * Get all memories across all stores, tagged with their source.
+     */
+    async getAllMemories() {
+        const allMemories = [];
+        for (const resolved of this.stores) {
+            const memories = await resolved.store.getAllMemories();
+            for (const m of memories) {
+                allMemories.push({
+                    ...m,
+                    sourceLayer: resolved.layer,
+                    sourceLabel: resolved.label,
+                });
+            }
+        }
+        return allMemories;
+    }
+    /**
+     * Read a memory, searching stores in precedence order.
+     * Path format: "layer:category/filename.md" or just "category/filename.md" (searches all).
+     */
+    async readMemory(memPath) {
+        // Check if path includes a layer prefix
+        const layerMatch = memPath.match(/^(project|personal|global|optional(?::[^:]+)?):(.+)/);
+        if (layerMatch) {
+            const targetLabel = layerMatch[1];
+            const filePath = layerMatch[2];
+            const resolved = this.stores.find((s) => s.label === targetLabel || s.layer === targetLabel);
+            if (!resolved)
+                return null;
+            const memory = await resolved.store.readMemory(filePath);
+            if (!memory)
+                return null;
+            return { ...memory, sourceLayer: resolved.layer, sourceLabel: resolved.label };
+        }
+        // No layer prefix — search in precedence order
+        for (const resolved of this.stores) {
+            const memory = await resolved.store.readMemory(memPath);
+            if (memory) {
+                return { ...memory, sourceLayer: resolved.layer, sourceLabel: resolved.label };
+            }
+        }
+        return null;
+    }
+    /**
+     * Get the writable store for a given target layer.
+     *
+     * When no target is specified, auto-selects: project → personal.
+     * Global is writable but NEVER auto-selected — it must be explicitly
+     * requested (store: "global"). This prevents accidental writes to
+     * shared org knowledge.
+     * Optional stores are always read-only.
+     */
+    getWriteTarget(target) {
+        if (target) {
+            const store = this.stores.find((s) => s.layer === target && s.writable);
+            return store || null;
+        }
+        // Default: project first, then personal. Never global (requires explicit intent).
+        const project = this.stores.find((s) => s.layer === "project");
+        if (project?.writable)
+            return project;
+        const personal = this.stores.find((s) => s.layer === "personal");
+        if (personal?.writable)
+            return personal;
+        return null;
+    }
+    /**
+     * Get a summary of all active stores for logging.
+     */
+    getSummary() {
+        if (this.stores.length === 0) {
+            return "No stores found. Create a .gnosys/ directory or set GNOSYS_PERSONAL.";
+        }
+        return this.stores
+            .map((s) => `[${s.label}] ${s.path} (${s.writable ? "read-write" : "read-only"})`)
+            .join("\n");
+    }
+    /**
+     * Register a project directory in the persistent project registry.
+     * Called by gnosys_init after creating a new store.
+     */
+    async registerProject(projectDir) {
+        const configPath = this.getRegistryPath();
+        let projects = [];
+        try {
+            const raw = await fs.readFile(configPath, "utf-8");
+            projects = JSON.parse(raw);
+        }
+        catch {
+            // File doesn't exist yet — that's fine
+        }
+        const resolved = path.resolve(projectDir);
+        if (!projects.includes(resolved)) {
+            projects.push(resolved);
+            await fs.mkdir(path.dirname(configPath), { recursive: true });
+            await fs.writeFile(configPath, JSON.stringify(projects, null, 2), "utf-8");
+        }
+    }
+    /**
+     * Directly add a project store to the active stores list.
+     * Used after gnosys_init creates a store, to avoid re-resolving from cwd.
+     */
+    async addProjectStore(storePath) {
+        // Remove any existing project store first
+        this.stores = this.stores.filter((s) => s.layer !== "project");
+        const store = new GnosysStore(storePath);
+        await store.init();
+        this.stores.unshift({
+            layer: "project",
+            label: "project",
+            store,
+            writable: true,
+            path: storePath,
+        });
+    }
+    /**
+     * Find a project store. Checks registered projects first (from
+     * ~/.config/gnosys/projects.json), then walks up from cwd as fallback.
+     */
+    async findProjectStore() {
+        // Check registered projects first — most reliable when MCP server
+        // cwd doesn't match the editor's open project.
+        const registered = await this.getRegisteredProjects();
+        for (const projectDir of registered) {
+            const candidate = path.join(projectDir, ".gnosys");
+            if (await this.isValidStore(candidate)) {
+                return candidate;
+            }
+        }
+        // Fallback: walk up from cwd (works when cwd matches the project)
+        let dir = path.resolve(process.cwd());
+        const root = path.parse(dir).root;
+        while (dir !== root) {
+            const candidate = path.join(dir, ".gnosys");
+            if (await this.isValidStore(candidate)) {
+                return candidate;
+            }
+            dir = path.dirname(dir);
+        }
+        return null;
+    }
+    /**
+     * Read registered project directories from persistent config.
+     */
+    async getRegisteredProjects() {
+        try {
+            const raw = await fs.readFile(this.getRegistryPath(), "utf-8");
+            return JSON.parse(raw);
+        }
+        catch {
+            return [];
+        }
+    }
+    /**
+     * Path to the persistent project registry file.
+     */
+    getRegistryPath() {
+        const home = process.env.HOME || process.env.USERPROFILE || "/tmp";
+        return path.join(home, ".config", "gnosys", "projects.json");
+    }
+    /**
+     * Check if a path looks like a valid Gnosys store.
+     */
+    async isValidStore(storePath) {
+        try {
+            const stat = await fs.stat(storePath);
+            return stat.isDirectory();
+        }
+        catch {
+            return false;
+        }
+    }
+}
+//# sourceMappingURL=resolver.js.map

package/dist/lib/resolver.js.map

@@ -0,0 +1 @@
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