gnosys-mcp 0.1.0

package/dist/lib/timeline.js

@@ -0,0 +1,116 @@
+/**
+ * Gnosys Timeline — Temporal views and statistics for memory stores.
+ *
+ * Group memories by time period to see knowledge evolution.
+ * Compute summary statistics across the store.
+ */
+/**
+ * Group memories by time period based on their created/modified dates.
+ */
+export function groupByPeriod(memories, period) {
+    const createdMap = new Map();
+    const modifiedMap = new Map();
+    for (const m of memories) {
+        const createdKey = toPeriodKey(m.frontmatter.created, period);
+        if (createdKey) {
+            const entry = createdMap.get(createdKey) || { count: 0, titles: [] };
+            entry.count++;
+            entry.titles.push(m.frontmatter.title);
+            createdMap.set(createdKey, entry);
+        }
+        const modifiedKey = toPeriodKey(m.frontmatter.modified, period);
+        if (modifiedKey && modifiedKey !== createdKey) {
+            modifiedMap.set(modifiedKey, (modifiedMap.get(modifiedKey) || 0) + 1);
+        }
+    }
+    // Merge all period keys
+    const allKeys = new Set([...createdMap.keys(), ...modifiedMap.keys()]);
+    const entries = [];
+    for (const key of allKeys) {
+        const created = createdMap.get(key);
+        entries.push({
+            period: key,
+            created: created?.count || 0,
+            modified: modifiedMap.get(key) || 0,
+            titles: created?.titles || [],
+        });
+    }
+    return entries.sort((a, b) => a.period.localeCompare(b.period));
+}
+/**
+ * Compute summary statistics across all memories.
+ */
+export function computeStats(memories) {
+    const byCategory = {};
+    const byStatus = {};
+    const byAuthor = {};
+    const byAuthority = {};
+    let totalConfidence = 0;
+    let oldest = null;
+    let newest = null;
+    let lastMod = null;
+    for (const m of memories) {
+        const fm = m.frontmatter;
+        byCategory[fm.category] = (byCategory[fm.category] || 0) + 1;
+        byStatus[fm.status] = (byStatus[fm.status] || 0) + 1;
+        byAuthor[fm.author] = (byAuthor[fm.author] || 0) + 1;
+        byAuthority[fm.authority] = (byAuthority[fm.authority] || 0) + 1;
+        totalConfidence += fm.confidence;
+        if (!oldest || fm.created < oldest)
+            oldest = fm.created;
+        if (!newest || fm.created > newest)
+            newest = fm.created;
+        if (!lastMod || fm.modified > lastMod)
+            lastMod = fm.modified;
+    }
+    return {
+        totalCount: memories.length,
+        byCategory,
+        byStatus,
+        byAuthor,
+        byAuthority,
+        averageConfidence: memories.length > 0 ? Math.round((totalConfidence / memories.length) * 100) / 100 : 0,
+        oldestCreated: oldest,
+        newestCreated: newest,
+        lastModified: lastMod,
+    };
+}
+/**
+ * Convert an ISO date string to a period key.
+ */
+function toPeriodKey(dateStr, period) {
+    if (!dateStr)
+        return null;
+    // Parse the date string (YYYY-MM-DD format)
+    const parts = dateStr.split("-");
+    if (parts.length < 3)
+        return null;
+    const year = parseInt(parts[0]);
+    const month = parseInt(parts[1]);
+    const day = parseInt(parts[2]);
+    switch (period) {
+        case "day":
+            return dateStr; // Already YYYY-MM-DD
+        case "week": {
+            const d = new Date(year, month - 1, day);
+            const weekNum = getISOWeek(d);
+            return `${year}-W${String(weekNum).padStart(2, "0")}`;
+        }
+        case "month":
+            return `${year}-${String(month).padStart(2, "0")}`;
+        case "year":
+            return `${year}`;
+    }
+}
+/**
+ * Get ISO week number for a date.
+ */
+function getISOWeek(d) {
+    const date = new Date(d.getTime());
+    date.setHours(0, 0, 0, 0);
+    date.setDate(date.getDate() + 3 - ((date.getDay() + 6) % 7));
+    const week1 = new Date(date.getFullYear(), 0, 4);
+    return (1 +
+        Math.round(((date.getTime() - week1.getTime()) / 86400000 - 3 + ((week1.getDay() + 6) % 7)) / 7));
+}
+//# sourceMappingURL=timeline.js.map

package/dist/lib/timeline.js.map

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

@@ -0,0 +1,63 @@
+/**
+ * Gnosys Wikilinks — Obsidian-compatible cross-references between memories.
+ *
+ * Scans memory content for [[wikilinks]] and builds a link graph.
+ * Supports both [[title]] and [[path|display text]] formats.
+ */
+import { Memory } from "./store.js";
+/** A single link found in a memory. */
+export interface WikiLink {
+    /** The raw target inside [[ ]] — could be a title or relative path */
+    target: string;
+    /** Optional display text (from [[target|display]]) */
+    displayText: string | null;
+    /** The source memory's relative path */
+    sourcePath: string;
+    /** The source memory's title */
+    sourceTitle: string;
+}
+/** A node in the link graph with both outgoing and incoming links. */
+export interface LinkNode {
+    /** This memory's relative path */
+    path: string;
+    /** This memory's title */
+    title: string;
+    /** Links going OUT from this memory */
+    outgoing: WikiLink[];
+    /** Backlinks coming IN to this memory */
+    incoming: WikiLink[];
+}
+/** Full link graph across all memories. */
+export interface LinkGraph {
+    nodes: Map<string, LinkNode>;
+    /** Total number of wikilinks found */
+    totalLinks: number;
+    /** Targets that don't resolve to any known memory */
+    orphanedLinks: WikiLink[];
+}
+/**
+ * Extract all wikilinks from a memory's content.
+ */
+export declare function extractLinks(memory: Memory): WikiLink[];
+/**
+ * Resolve a wikilink target to a memory.
+ * Tries matching by: exact relative path, title (case-insensitive), id.
+ */
+export declare function resolveLink(target: string, memories: Memory[]): Memory | null;
+/**
+ * Build a full link graph from all memories.
+ */
+export declare function buildLinkGraph(memories: Memory[]): LinkGraph;
+/**
+ * Get backlinks for a specific memory.
+ */
+export declare function getBacklinks(memories: Memory[], targetPath: string): WikiLink[];
+/**
+ * Get outgoing links for a specific memory.
+ */
+export declare function getOutgoingLinks(memories: Memory[], sourcePath: string): WikiLink[];
+/**
+ * Format the link graph as a simple text summary.
+ */
+export declare function formatGraphSummary(graph: LinkGraph): string;
+//# sourceMappingURL=wikilinks.d.ts.map

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

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package/dist/lib/wikilinks.js

@@ -0,0 +1,146 @@
+/**
+ * Gnosys Wikilinks — Obsidian-compatible cross-references between memories.
+ *
+ * Scans memory content for [[wikilinks]] and builds a link graph.
+ * Supports both [[title]] and [[path|display text]] formats.
+ */
+// Regex to match [[target]] or [[target|display text]]
+const WIKILINK_RE = /\[\[([^\]|]+?)(?:\|([^\]]+?))?\]\]/g;
+/**
+ * Extract all wikilinks from a memory's content.
+ */
+export function extractLinks(memory) {
+    const links = [];
+    let match;
+    // Reset regex state
+    WIKILINK_RE.lastIndex = 0;
+    while ((match = WIKILINK_RE.exec(memory.content)) !== null) {
+        links.push({
+            target: match[1].trim(),
+            displayText: match[2]?.trim() || null,
+            sourcePath: memory.relativePath,
+            sourceTitle: memory.frontmatter.title,
+        });
+    }
+    return links;
+}
+/**
+ * Resolve a wikilink target to a memory.
+ * Tries matching by: exact relative path, title (case-insensitive), id.
+ */
+export function resolveLink(target, memories) {
+    // 1. Exact relative path match
+    const byPath = memories.find((m) => m.relativePath === target);
+    if (byPath)
+        return byPath;
+    // 2. Path with .md extension
+    const withMd = memories.find((m) => m.relativePath === target + ".md");
+    if (withMd)
+        return withMd;
+    // 3. Filename match (target might be just the filename without category dir)
+    const byFilename = memories.find((m) => {
+        const filename = m.relativePath.split("/").pop()?.replace(/\.md$/, "");
+        return filename === target;
+    });
+    if (byFilename)
+        return byFilename;
+    // 4. Title match (case-insensitive)
+    const lowerTarget = target.toLowerCase();
+    const byTitle = memories.find((m) => m.frontmatter.title.toLowerCase() === lowerTarget);
+    if (byTitle)
+        return byTitle;
+    // 5. ID match
+    const byId = memories.find((m) => m.frontmatter.id === target);
+    if (byId)
+        return byId;
+    return null;
+}
+/**
+ * Build a full link graph from all memories.
+ */
+export function buildLinkGraph(memories) {
+    const nodes = new Map();
+    const orphanedLinks = [];
+    let totalLinks = 0;
+    // Initialize nodes for all memories
+    for (const m of memories) {
+        nodes.set(m.relativePath, {
+            path: m.relativePath,
+            title: m.frontmatter.title,
+            outgoing: [],
+            incoming: [],
+        });
+    }
+    // Extract links and resolve them
+    for (const m of memories) {
+        const links = extractLinks(m);
+        totalLinks += links.length;
+        for (const link of links) {
+            const resolved = resolveLink(link.target, memories);
+            if (resolved) {
+                // Add outgoing link to source
+                const sourceNode = nodes.get(m.relativePath);
+                sourceNode.outgoing.push(link);
+                // Add backlink to target
+                const targetNode = nodes.get(resolved.relativePath);
+                targetNode.incoming.push(link);
+            }
+            else {
+                orphanedLinks.push(link);
+            }
+        }
+    }
+    return { nodes, totalLinks, orphanedLinks };
+}
+/**
+ * Get backlinks for a specific memory.
+ */
+export function getBacklinks(memories, targetPath) {
+    const graph = buildLinkGraph(memories);
+    const node = graph.nodes.get(targetPath);
+    return node?.incoming || [];
+}
+/**
+ * Get outgoing links for a specific memory.
+ */
+export function getOutgoingLinks(memories, sourcePath) {
+    const graph = buildLinkGraph(memories);
+    const node = graph.nodes.get(sourcePath);
+    return node?.outgoing || [];
+}
+/**
+ * Format the link graph as a simple text summary.
+ */
+export function formatGraphSummary(graph) {
+    const lines = [];
+    lines.push(`Link Graph: ${graph.totalLinks} total links, ${graph.orphanedLinks.length} orphaned\n`);
+    // Find most-connected nodes
+    const connected = Array.from(graph.nodes.values())
+        .filter((n) => n.outgoing.length > 0 || n.incoming.length > 0)
+        .sort((a, b) => (b.incoming.length + b.outgoing.length) - (a.incoming.length + a.outgoing.length));
+    if (connected.length === 0) {
+        lines.push("No cross-references found. Use [[Title]] in memory content to create links.");
+        return lines.join("\n");
+    }
+    for (const node of connected) {
+        lines.push(`**${node.title}** (${node.path})`);
+        lines.push(`  → ${node.outgoing.length} outgoing, ← ${node.incoming.length} backlinks`);
+        if (node.outgoing.length > 0) {
+            const targets = node.outgoing.map((l) => l.displayText || l.target).join(", ");
+            lines.push(`  Links to: ${targets}`);
+        }
+        if (node.incoming.length > 0) {
+            const sources = node.incoming.map((l) => l.sourceTitle).join(", ");
+            lines.push(`  Referenced by: ${sources}`);
+        }
+        lines.push("");
+    }
+    if (graph.orphanedLinks.length > 0) {
+        lines.push("Orphaned links (targets not found):");
+        for (const link of graph.orphanedLinks) {
+            lines.push(`  [[${link.target}]] in ${link.sourceTitle}`);
+        }
+    }
+    return lines.join("\n");
+}
+//# sourceMappingURL=wikilinks.js.map

package/dist/lib/wikilinks.js.map

@@ -0,0 +1 @@
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package/dist/test/bootstrap.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=bootstrap.test.d.ts.map

package/dist/test/bootstrap.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"bootstrap.test.d.ts","sourceRoot":"","sources":["../../src/test/bootstrap.test.ts"],"names":[],"mappings":""}

package/dist/test/bootstrap.test.js

@@ -0,0 +1,208 @@
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import fs from "fs/promises";
+import path from "path";
+import os from "os";
+import { discoverFiles, parseFileForImport, bootstrap } from "../lib/bootstrap.js";
+import { GnosysStore } from "../lib/store.js";
+let tempDir;
+let sourceDir;
+let storeDir;
+beforeEach(async () => {
+    tempDir = await fs.mkdtemp(path.join(os.tmpdir(), "gnosys-bootstrap-test-"));
+    sourceDir = path.join(tempDir, "source");
+    storeDir = path.join(tempDir, "store");
+    await fs.mkdir(sourceDir, { recursive: true });
+    await fs.mkdir(storeDir, { recursive: true });
+});
+afterEach(async () => {
+    await fs.rm(tempDir, { recursive: true, force: true });
+});
+describe("discoverFiles", () => {
+    it("finds markdown files", async () => {
+        await fs.writeFile(path.join(sourceDir, "doc1.md"), "# Doc 1");
+        await fs.writeFile(path.join(sourceDir, "doc2.md"), "# Doc 2");
+        await fs.writeFile(path.join(sourceDir, "readme.txt"), "Not markdown");
+        const files = await discoverFiles(sourceDir);
+        expect(files).toHaveLength(2);
+        expect(files).toContain("doc1.md");
+        expect(files).toContain("doc2.md");
+    });
+    it("finds files in subdirectories", async () => {
+        await fs.mkdir(path.join(sourceDir, "decisions"), { recursive: true });
+        await fs.writeFile(path.join(sourceDir, "decisions", "auth.md"), "# Auth");
+        const files = await discoverFiles(sourceDir);
+        expect(files).toHaveLength(1);
+        expect(files[0]).toBe("decisions/auth.md");
+    });
+    it("supports custom patterns", async () => {
+        await fs.writeFile(path.join(sourceDir, "doc.md"), "# Doc");
+        await fs.writeFile(path.join(sourceDir, "notes.txt"), "Notes");
+        const files = await discoverFiles(sourceDir, ["**/*.md", "**/*.txt"]);
+        expect(files).toHaveLength(2);
+    });
+    it("returns empty for empty directory", async () => {
+        const files = await discoverFiles(sourceDir);
+        expect(files).toHaveLength(0);
+    });
+    it("deduplicates files across patterns", async () => {
+        await fs.writeFile(path.join(sourceDir, "doc.md"), "# Doc");
+        const files = await discoverFiles(sourceDir, ["**/*.md", "*.md"]);
+        expect(files).toHaveLength(1);
+    });
+});
+describe("parseFileForImport", () => {
+    const defaultOpts = {
+        sourceDir: "/tmp",
+        defaultCategory: "imported",
+        preserveFrontmatter: false,
+    };
+    it("extracts title from H1 heading", () => {
+        const { frontmatter } = parseFileForImport("# My Decision\n\nContent here.", "doc.md", defaultOpts);
+        expect(frontmatter.title).toBe("My Decision");
+    });
+    it("falls back to filename for title", () => {
+        const { frontmatter } = parseFileForImport("No heading here.", "my-cool-doc.md", defaultOpts);
+        expect(frontmatter.title).toBe("My Cool Doc");
+    });
+    it("infers category from directory structure", () => {
+        const { frontmatter } = parseFileForImport("# Test", "decisions/auth.md", defaultOpts);
+        expect(frontmatter.category).toBe("decisions");
+    });
+    it("uses default category for root files", () => {
+        const { frontmatter } = parseFileForImport("# Test", "doc.md", defaultOpts);
+        expect(frontmatter.category).toBe("imported");
+    });
+    it("preserves existing frontmatter when option is set", () => {
+        const content = `---
+title: Custom Title
+category: architecture
+confidence: 0.95
+author: human
+---
+# Custom Title
+
+Content here.`;
+        const { frontmatter } = parseFileForImport(content, "doc.md", {
+            ...defaultOpts,
+            preserveFrontmatter: true,
+        });
+        expect(frontmatter.title).toBe("Custom Title");
+        expect(frontmatter.category).toBe("architecture");
+        expect(frontmatter.confidence).toBe(0.95);
+        expect(frontmatter.author).toBe("human");
+    });
+    it("uses defaults when not preserving frontmatter", () => {
+        const content = `---
+title: Custom Title
+category: architecture
+---
+# Custom Title`;
+        const { frontmatter } = parseFileForImport(content, "doc.md", defaultOpts);
+        // Should NOT preserve even though frontmatter exists
+        expect(frontmatter.category).toBe("imported");
+        expect(frontmatter.authority).toBe("imported");
+    });
+    it("strips frontmatter from body", () => {
+        const content = `---
+title: Test
+---
+# Test
+
+Body content.`;
+        const { body } = parseFileForImport(content, "doc.md", defaultOpts);
+        expect(body).toBe("# Test\n\nBody content.");
+        expect(body).not.toContain("---");
+    });
+});
+describe("bootstrap", () => {
+    it("imports files into the store", async () => {
+        await fs.writeFile(path.join(sourceDir, "doc1.md"), "# First Doc\n\nContent one.");
+        await fs.writeFile(path.join(sourceDir, "doc2.md"), "# Second Doc\n\nContent two.");
+        const store = new GnosysStore(storeDir);
+        await store.init();
+        const result = await bootstrap(store, {
+            sourceDir,
+            defaultCategory: "imported",
+        });
+        expect(result.totalScanned).toBe(2);
+        expect(result.imported).toHaveLength(2);
+        expect(result.skipped).toHaveLength(0);
+        expect(result.failed).toHaveLength(0);
+        // Verify files were written
+        const memories = await store.getAllMemories();
+        expect(memories).toHaveLength(2);
+    });
+    it("skips existing memories when skipExisting is true", async () => {
+        const store = new GnosysStore(storeDir);
+        await store.init();
+        // Write a memory first
+        await store.writeMemory("imported", "first-doc.md", {
+            id: "existing-1",
+            title: "First Doc",
+            category: "imported",
+            tags: { domain: [] },
+            relevance: "",
+            author: "human",
+            authority: "imported",
+            confidence: 0.7,
+            created: "2026-03-01",
+            modified: "2026-03-01",
+            status: "active",
+            supersedes: null,
+        }, "# First Doc\n\nExisting content.");
+        // Now try to bootstrap with the same title
+        await fs.writeFile(path.join(sourceDir, "doc1.md"), "# First Doc\n\nNew content.");
+        await fs.writeFile(path.join(sourceDir, "doc2.md"), "# Second Doc\n\nContent two.");
+        const result = await bootstrap(store, {
+            sourceDir,
+            skipExisting: true,
+            defaultCategory: "imported",
+        });
+        expect(result.imported).toHaveLength(1);
+        expect(result.skipped).toHaveLength(1);
+        expect(result.skipped[0]).toBe("doc1.md");
+    });
+    it("supports dry run mode", async () => {
+        await fs.writeFile(path.join(sourceDir, "doc1.md"), "# Test\n\nContent.");
+        const store = new GnosysStore(storeDir);
+        await store.init();
+        const result = await bootstrap(store, {
+            sourceDir,
+            dryRun: true,
+        });
+        expect(result.imported).toHaveLength(1);
+        // Verify nothing was actually written
+        const memories = await store.getAllMemories();
+        expect(memories).toHaveLength(0);
+    });
+    it("handles empty source directory", async () => {
+        const store = new GnosysStore(storeDir);
+        await store.init();
+        const result = await bootstrap(store, { sourceDir });
+        expect(result.totalScanned).toBe(0);
+        expect(result.imported).toHaveLength(0);
+    });
+    it("respects custom patterns", async () => {
+        await fs.writeFile(path.join(sourceDir, "doc.md"), "# MD");
+        await fs.writeFile(path.join(sourceDir, "notes.txt"), "TXT content");
+        const store = new GnosysStore(storeDir);
+        await store.init();
+        const result = await bootstrap(store, {
+            sourceDir,
+            patterns: ["**/*.txt"],
+        });
+        expect(result.totalScanned).toBe(1);
+        expect(result.imported).toHaveLength(1);
+    });
+    it("preserves category from subdirectory structure", async () => {
+        await fs.mkdir(path.join(sourceDir, "architecture"), { recursive: true });
+        await fs.writeFile(path.join(sourceDir, "architecture", "layers.md"), "# Three Layers\n\nContent.");
+        const store = new GnosysStore(storeDir);
+        await store.init();
+        await bootstrap(store, { sourceDir });
+        const memories = await store.getAllMemories();
+        expect(memories).toHaveLength(1);
+        expect(memories[0].frontmatter.category).toBe("architecture");
+    });
+});
+//# sourceMappingURL=bootstrap.test.js.map

package/dist/test/bootstrap.test.js.map

@@ -0,0 +1 @@
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package/dist/test/history.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=history.test.d.ts.map

package/dist/test/history.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"history.test.d.ts","sourceRoot":"","sources":["../../src/test/history.test.ts"],"names":[],"mappings":""}