gnosys-mcp 2.3.0 → 2.5.0

package/dist/cli.js

@@ -8,6 +8,7 @@ import path from "path";
 import fs from "fs/promises";
 import { fileURLToPath } from "url";
 import dotenv from "dotenv";
+import { readFileSync } from "fs";
 import { GnosysResolver } from "./lib/resolver.js";
 import { GnosysSearch } from "./lib/search.js";
 import { GnosysTagRegistry } from "./lib/tags.js";
@@ -25,14 +26,37 @@ import { GnosysAsk } from "./lib/ask.js";
 import { getLLMProvider, isProviderAvailable } from "./lib/llm.js";
 import { GnosysDB } from "./lib/db.js";
 import { migrate, formatMigrationReport } from "./lib/migrate.js";
-import { createProjectIdentity, readProjectIdentity } from "./lib/projectIdentity.js";
+import { createProjectIdentity, readProjectIdentity, findProjectIdentity } from "./lib/projectIdentity.js";
 import { setPreference, getPreference, getAllPreferences, deletePreference } from "./lib/preferences.js";
 import { syncRules } from "./lib/rulesGen.js";
 // Load API keys from ~/.config/gnosys/.env (same as MCP server)
+// IMPORTANT: We use dotenv.parse() instead of dotenv.config() because
+// dotenv v17+ writes injection notices to stdout, which corrupts
+// --json output and piped usage. parse() is a pure function with no side effects.
 const home = process.env.HOME || process.env.USERPROFILE || "/tmp";
-dotenv.config({ path: path.join(home, ".config", "gnosys", ".env") });
-// Also load .env from current directory as fallback
-dotenv.config();
+try {
+    const envFile = readFileSync(path.join(home, ".config", "gnosys", ".env"), "utf8");
+    const parsed = dotenv.parse(envFile);
+    for (const [key, val] of Object.entries(parsed)) {
+        if (!(key in process.env))
+            process.env[key] = val;
+    }
+}
+catch {
+    // .env file not found — that's fine, env vars may be set elsewhere
+}
+// Also try .env from current directory as fallback
+try {
+    const localEnv = readFileSync(".env", "utf8");
+    const localParsed = dotenv.parse(localEnv);
+    for (const [key, val] of Object.entries(localParsed)) {
+        if (!(key in process.env))
+            process.env[key] = val;
+    }
+}
+catch {
+    // No local .env — fine
+}
 // Read version from package.json at build time
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -44,6 +68,26 @@ async function getResolver() {
     await resolver.resolve();
     return resolver;
 }
+/**
+ * v3.0: Resolve projectId from nearest .gnosys/gnosys.json.
+ * Used by CLI write commands to tag memories with the correct project.
+ */
+async function resolveProjectId(dir) {
+    const result = await findProjectIdentity(dir || process.cwd());
+    return result?.identity.projectId || null;
+}
+/**
+ * Output helper: if --json flag is set, output JSON; otherwise call the
+ * human-readable formatter function.
+ */
+function outputResult(json, data, humanFn) {
+    if (json) {
+        console.log(JSON.stringify(data, null, 2));
+    }
+    else {
+        humanFn();
+    }
+}
 program
     .name("gnosys")
     .description("Gnosys — Agent-first persistent memory system (SQLite core + Dream Mode + Obsidian export)")
@@ -52,7 +96,8 @@ program
 program
     .command("read <memoryPath>")
     .description("Read a specific memory. Supports layer prefix (e.g., project:decisions/auth.md)")
-    .action(async (memoryPath) => {
+    .option("--json", "Output as JSON")
+    .action(async (memoryPath, opts) => {
     const resolver = await getResolver();
     const memory = await resolver.readMemory(memoryPath);
     if (!memory) {
@@ -60,14 +105,17 @@ program
         process.exit(1);
     }
     const raw = await fs.readFile(memory.filePath, "utf-8");
-    console.log(`[Source: ${memory.sourceLabel}]\n`);
-    console.log(raw);
+    outputResult(!!opts.json, { path: memoryPath, source: memory.sourceLabel, content: raw }, () => {
+        console.log(`[Source: ${memory.sourceLabel}]\n`);
+        console.log(raw);
+    });
 });
 // ─── gnosys discover <query> ─────────────────────────────────────────────
 program
     .command("discover <query>")
     .description("Discover relevant memories by keyword. Searches relevance clouds, titles, and tags — returns metadata only, no content.")
     .option("-n, --limit <number>", "Max results", "20")
+    .option("--json", "Output as JSON")
     .action(async (query, opts) => {
     const resolver = await getResolver();
     const stores = resolver.getStores();
@@ -82,18 +130,22 @@ program
     }
     const results = search.discover(query, parseInt(opts.limit));
     if (results.length === 0) {
-        console.log(`No memories found for "${query}". Try gnosys search for full-text.`);
+        outputResult(!!opts.json, { query, results: [] }, () => {
+            console.log(`No memories found for "${query}". Try gnosys search for full-text.`);
+        });
         search.close();
         return;
     }
-    console.log(`Found ${results.length} relevant memories for "${query}":\n`);
-    for (const r of results) {
-        console.log(`  ${r.title}`);
-        console.log(`  ${r.relative_path}`);
-        if (r.relevance)
-            console.log(`  Relevance: ${r.relevance}`);
-        console.log();
-    }
+    outputResult(!!opts.json, { query, count: results.length, results }, () => {
+        console.log(`Found ${results.length} relevant memories for "${query}":\n`);
+        for (const r of results) {
+            console.log(`  ${r.title}`);
+            console.log(`  ${r.relative_path}`);
+            if (r.relevance)
+                console.log(`  Relevance: ${r.relevance}`);
+            console.log();
+        }
+    });
     search.close();
 });
 // ─── gnosys search <query> ───────────────────────────────────────────────
@@ -101,6 +153,7 @@ program
     .command("search <query>")
     .description("Search memories by keyword across all stores")
     .option("-n, --limit <number>", "Max results", "20")
+    .option("--json", "Output as JSON")
     .action(async (query, opts) => {
     const resolver = await getResolver();
     const stores = resolver.getStores();
@@ -115,17 +168,21 @@ program
     }
     const results = search.search(query, parseInt(opts.limit));
     if (results.length === 0) {
-        console.log(`No results for "${query}".`);
+        outputResult(!!opts.json, { query, results: [] }, () => {
+            console.log(`No results for "${query}".`);
+        });
         search.close();
         return;
     }
-    console.log(`Found ${results.length} results for "${query}":\n`);
-    for (const r of results) {
-        console.log(`  ${r.title}`);
-        console.log(`  ${r.relative_path}`);
-        console.log(`  ${r.snippet.replace(/>>>/g, "").replace(/<<</g, "")}`);
-        console.log();
-    }
+    outputResult(!!opts.json, { query, count: results.length, results }, () => {
+        console.log(`Found ${results.length} results for "${query}":\n`);
+        for (const r of results) {
+            console.log(`  ${r.title}`);
+            console.log(`  ${r.relative_path}`);
+            console.log(`  ${r.snippet.replace(/>>>/g, "").replace(/<<</g, "")}`);
+            console.log();
+        }
+    });
     search.close();
 });
 // ─── gnosys list ─────────────────────────────────────────────────────────
@@ -135,6 +192,7 @@ program
     .option("-c, --category <category>", "Filter by category")
     .option("-t, --tag <tag>", "Filter by tag")
     .option("-s, --store <store>", "Filter by store layer")
+    .option("--json", "Output as JSON")
     .action(async (opts) => {
     const resolver = await getResolver();
     let memories = await resolver.getAllMemories();
@@ -152,12 +210,24 @@ program
             return tags.includes(opts.tag);
         });
     }
-    console.log(`${memories.length} memories:\n`);
-    for (const m of memories) {
-        console.log(`  [${m.sourceLabel}] [${m.frontmatter.status}] ${m.frontmatter.title}`);
-        console.log(`    ${m.sourceLabel}:${m.relativePath}`);
-        console.log();
-    }
+    outputResult(!!opts.json, {
+        count: memories.length,
+        memories: memories.map((m) => ({
+            id: m.frontmatter.id,
+            title: m.frontmatter.title,
+            category: m.frontmatter.category,
+            status: m.frontmatter.status,
+            source: m.sourceLabel,
+            path: `${m.sourceLabel}:${m.relativePath}`,
+        })),
+    }, () => {
+        console.log(`${memories.length} memories:\n`);
+        for (const m of memories) {
+            console.log(`  [${m.sourceLabel}] [${m.frontmatter.status}] ${m.frontmatter.title}`);
+            console.log(`    ${m.sourceLabel}:${m.relativePath}`);
+            console.log();
+        }
+    });
 });
 // ─── gnosys add <input> ──────────────────────────────────────────────────
 program
@@ -830,31 +900,36 @@ program
 program
     .command("stats")
     .description("Show summary statistics for the memory store")
-    .action(async () => {
+    .option("--json", "Output as JSON")
+    .action(async (opts) => {
     const resolver = await getResolver();
     const allMemories = await resolver.getAllMemories();
     if (allMemories.length === 0) {
-        console.log("No memories found.");
+        outputResult(!!opts.json, { totalCount: 0 }, () => {
+            console.log("No memories found.");
+        });
         return;
     }
     const stats = computeStats(allMemories);
-    console.log(`Gnosys Store Statistics:\n`);
-    console.log(`  Total memories: ${stats.totalCount}`);
-    console.log(`  Average confidence: ${stats.averageConfidence}`);
-    console.log(`  Date range: ${stats.oldestCreated} → ${stats.newestCreated}`);
-    console.log(`  Last modified: ${stats.lastModified}`);
-    console.log(`\n  By category:`);
-    for (const [cat, count] of Object.entries(stats.byCategory).sort((a, b) => b[1] - a[1])) {
-        console.log(`    ${cat}: ${count}`);
-    }
-    console.log(`\n  By status:`);
-    for (const [st, count] of Object.entries(stats.byStatus)) {
-        console.log(`    ${st}: ${count}`);
-    }
-    console.log(`\n  By author:`);
-    for (const [author, count] of Object.entries(stats.byAuthor)) {
-        console.log(`    ${author}: ${count}`);
-    }
+    outputResult(!!opts.json, stats, () => {
+        console.log(`Gnosys Store Statistics:\n`);
+        console.log(`  Total memories: ${stats.totalCount}`);
+        console.log(`  Average confidence: ${stats.averageConfidence}`);
+        console.log(`  Date range: ${stats.oldestCreated} → ${stats.newestCreated}`);
+        console.log(`  Last modified: ${stats.lastModified}`);
+        console.log(`\n  By category:`);
+        for (const [cat, count] of Object.entries(stats.byCategory).sort((a, b) => b[1] - a[1])) {
+            console.log(`    ${cat}: ${count}`);
+        }
+        console.log(`\n  By status:`);
+        for (const [st, count] of Object.entries(stats.byStatus)) {
+            console.log(`    ${st}: ${count}`);
+        }
+        console.log(`\n  By author:`);
+        for (const [author, count] of Object.entries(stats.byAuthor)) {
+            console.log(`    ${author}: ${count}`);
+        }
+    });
 });
 // ─── gnosys links <path> ─────────────────────────────────────────────────
 program
@@ -2128,7 +2203,8 @@ program
 program
     .command("projects")
     .description("List all registered projects in the central DB")
-    .action(async () => {
+    .option("--json", "Output as JSON")
+    .action(async (opts) => {
     let centralDb = null;
     try {
         centralDb = GnosysDB.openCentral();
@@ -2142,16 +2218,21 @@ program
             centralDb.close();
             return;
         }
-        console.log(`${projects.length} registered project(s):\n`);
-        for (const p of projects) {
-            const memCount = centralDb.getMemoriesByProject(p.id).length;
-            console.log(`  ${p.name}`);
-            console.log(`    ID:        ${p.id}`);
-            console.log(`    Directory: ${p.working_directory}`);
-            console.log(`    Memories:  ${memCount}`);
-            console.log(`    Created:   ${p.created}`);
-            console.log();
-        }
+        const projectData = projects.map((p) => ({
+            ...p,
+            memoryCount: centralDb.getMemoriesByProject(p.id).length,
+        }));
+        outputResult(!!opts.json, { count: projects.length, projects: projectData }, () => {
+            console.log(`${projects.length} registered project(s):\n`);
+            for (const p of projectData) {
+                console.log(`  ${p.name}`);
+                console.log(`    ID:        ${p.id}`);
+                console.log(`    Directory: ${p.working_directory}`);
+                console.log(`    Memories:  ${p.memoryCount}`);
+                console.log(`    Created:   ${p.created}`);
+                console.log();
+            }
+        });
     }
     catch (err) {
         console.error(`Error: ${err instanceof Error ? err.message : err}`);
@@ -2196,7 +2277,8 @@ prefCmd
 prefCmd
     .command("get [key]")
     .description("Get a preference by key, or list all preferences if no key given.")
-    .action(async (key) => {
+    .option("--json", "Output as JSON")
+    .action(async (key, opts) => {
     let centralDb = null;
     try {
         centralDb = GnosysDB.openCentral();
@@ -2210,23 +2292,29 @@ prefCmd
                 console.log(`No preference found for key "${key}".`);
                 return;
             }
-            console.log(`${pref.title} (${pref.key})\n`);
-            console.log(pref.value);
-            console.log(`\nConfidence: ${pref.confidence}`);
-            console.log(`Modified: ${pref.modified}`);
+            outputResult(!!opts.json, pref, () => {
+                console.log(`${pref.title} (${pref.key})\n`);
+                console.log(pref.value);
+                console.log(`\nConfidence: ${pref.confidence}`);
+                console.log(`Modified: ${pref.modified}`);
+            });
         }
         else {
             const prefs = getAllPreferences(centralDb);
             if (prefs.length === 0) {
-                console.log("No preferences set. Use 'gnosys pref set <key> <value>' to add some.");
+                outputResult(!!opts.json, { preferences: [] }, () => {
+                    console.log("No preferences set. Use 'gnosys pref set <key> <value>' to add some.");
+                });
                 return;
             }
-            console.log(`${prefs.length} user preference(s):\n`);
-            for (const p of prefs) {
-                console.log(`  ${p.title} (${p.key})`);
-                console.log(`    ${p.value.split("\n")[0]}`);
-                console.log();
-            }
+            outputResult(!!opts.json, { count: prefs.length, preferences: prefs }, () => {
+                console.log(`${prefs.length} user preference(s):\n`);
+                for (const p of prefs) {
+                    console.log(`  ${p.title} (${p.key})`);
+                    console.log(`    ${p.value.split("\n")[0]}`);
+                    console.log();
+                }
+            });
         }
     }
     catch (err) {
@@ -2309,5 +2397,212 @@ program
         centralDb?.close();
     }
 });
+// ─── gnosys fsearch (federated search) ───────────────────────────────────
+program
+    .command("fsearch <query>")
+    .description("Federated search across all scopes with tier boosting (project > user > global)")
+    .option("-l, --limit <n>", "Max results", "20")
+    .option("-d, --directory <dir>", "Project directory for context")
+    .option("--no-global", "Exclude global-scope memories")
+    .option("--json", "Output as JSON")
+    .action(async (query, opts) => {
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        if (!centralDb.isAvailable()) {
+            console.error("Central DB not available.");
+            process.exit(1);
+        }
+        const { federatedSearch, detectCurrentProject } = await import("./lib/federated.js");
+        const projectId = await detectCurrentProject(centralDb, opts.directory || undefined);
+        const results = federatedSearch(centralDb, query, {
+            limit: parseInt(opts.limit, 10),
+            projectId,
+            includeGlobal: opts.global,
+        });
+        if (opts.json) {
+            console.log(JSON.stringify({ query, projectId, count: results.length, results }, null, 2));
+        }
+        else {
+            if (results.length === 0) {
+                console.log(`No results for "${query}".`);
+                return;
+            }
+            const ctx = projectId ? `Context: project ${projectId}` : "No project detected";
+            console.log(ctx);
+            for (const [i, r] of results.entries()) {
+                const proj = r.projectName ? ` [${r.projectName}]` : "";
+                console.log(`\n${i + 1}. ${r.title} (${r.category})${proj}`);
+                console.log(`   scope: ${r.scope} | score: ${r.score.toFixed(4)} | boosts: ${r.boosts.join(", ")}`);
+                if (r.snippet)
+                    console.log(`   ${r.snippet.substring(0, 120)}`);
+            }
+        }
+    }
+    catch (err) {
+        console.error(`Error: ${err instanceof Error ? err.message : err}`);
+        process.exit(1);
+    }
+    finally {
+        centralDb?.close();
+    }
+});
+// ─── gnosys ambiguity ────────────────────────────────────────────────────
+program
+    .command("ambiguity <query>")
+    .description("Check if a query matches memories in multiple projects")
+    .option("--json", "Output as JSON")
+    .action(async (query, opts) => {
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        if (!centralDb.isAvailable()) {
+            console.error("Central DB not available.");
+            process.exit(1);
+        }
+        const { detectAmbiguity } = await import("./lib/federated.js");
+        const ambiguity = detectAmbiguity(centralDb, query);
+        if (opts.json) {
+            console.log(JSON.stringify({ query, ambiguous: !!ambiguity, ...(ambiguity || {}) }, null, 2));
+        }
+        else if (!ambiguity) {
+            console.log(`No ambiguity for "${query}" — matches at most one project.`);
+        }
+        else {
+            console.log(ambiguity.message);
+            for (const c of ambiguity.candidates) {
+                console.log(`\n  ${c.projectName} (${c.projectId})`);
+                console.log(`    Dir: ${c.workingDirectory}`);
+                console.log(`    Matching memories: ${c.memoryCount}`);
+            }
+        }
+    }
+    catch (err) {
+        console.error(`Error: ${err instanceof Error ? err.message : err}`);
+        process.exit(1);
+    }
+    finally {
+        centralDb?.close();
+    }
+});
+// ─── gnosys briefing ─────────────────────────────────────────────────────
+program
+    .command("briefing")
+    .description("Generate project briefing — memory state summary, categories, recent activity, top tags")
+    .option("-p, --project <id>", "Project ID (auto-detects if omitted)")
+    .option("-a, --all", "Generate briefings for all projects")
+    .option("-d, --directory <dir>", "Project directory for auto-detection")
+    .option("--json", "Output as JSON")
+    .action(async (opts) => {
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        if (!centralDb.isAvailable()) {
+            console.error("Central DB not available.");
+            process.exit(1);
+        }
+        const { generateBriefing, generateAllBriefings, detectCurrentProject } = await import("./lib/federated.js");
+        if (opts.all) {
+            const briefings = generateAllBriefings(centralDb);
+            if (opts.json) {
+                console.log(JSON.stringify({ count: briefings.length, briefings }, null, 2));
+            }
+            else {
+                if (briefings.length === 0) {
+                    console.log("No projects registered.");
+                    return;
+                }
+                for (const b of briefings) {
+                    console.log(`\n## ${b.projectName}`);
+                    console.log(b.summary);
+                }
+            }
+            return;
+        }
+        let pid = opts.project || null;
+        if (!pid)
+            pid = await detectCurrentProject(centralDb, opts.directory || undefined);
+        if (!pid) {
+            console.error("No project specified and none detected.");
+            process.exit(1);
+        }
+        const briefing = generateBriefing(centralDb, pid);
+        if (!briefing) {
+            console.error(`Project not found: ${pid}`);
+            process.exit(1);
+        }
+        if (opts.json) {
+            console.log(JSON.stringify(briefing, null, 2));
+        }
+        else {
+            console.log(`# Briefing: ${briefing.projectName}`);
+            console.log(`Directory: ${briefing.workingDirectory}`);
+            console.log(`Active memories: ${briefing.activeMemories} / ${briefing.totalMemories}`);
+            console.log(`\nCategories:`);
+            for (const [cat, count] of Object.entries(briefing.categories).sort((a, b) => b[1] - a[1])) {
+                console.log(`  ${cat}: ${count}`);
+            }
+            console.log(`\nRecent activity (7d):`);
+            if (briefing.recentActivity.length === 0) {
+                console.log("  None");
+            }
+            for (const r of briefing.recentActivity) {
+                console.log(`  - ${r.title} (${r.modified})`);
+            }
+            console.log(`\nTop tags: ${briefing.topTags.slice(0, 10).map((t) => `${t.tag}(${t.count})`).join(", ") || "None"}`);
+            console.log(`\n${briefing.summary}`);
+        }
+    }
+    catch (err) {
+        console.error(`Error: ${err instanceof Error ? err.message : err}`);
+        process.exit(1);
+    }
+    finally {
+        centralDb?.close();
+    }
+});
+// ─── gnosys working-set ──────────────────────────────────────────────────
+program
+    .command("working-set")
+    .description("Show the implicit working set — recently modified memories for the current project")
+    .option("-d, --directory <dir>", "Project directory")
+    .option("-w, --window <hours>", "Lookback window in hours", "24")
+    .option("--json", "Output as JSON")
+    .action(async (opts) => {
+    let centralDb = null;
+    try {
+        centralDb = GnosysDB.openCentral();
+        if (!centralDb.isAvailable()) {
+            console.error("Central DB not available.");
+            process.exit(1);
+        }
+        const { getWorkingSet, formatWorkingSet, detectCurrentProject } = await import("./lib/federated.js");
+        const pid = await detectCurrentProject(centralDb, opts.directory || undefined);
+        if (!pid) {
+            console.error("No project detected.");
+            process.exit(1);
+        }
+        const windowHours = parseInt(opts.window, 10);
+        const workingSet = getWorkingSet(centralDb, pid, { windowHours });
+        if (opts.json) {
+            console.log(JSON.stringify({
+                projectId: pid,
+                windowHours,
+                count: workingSet.length,
+                memories: workingSet.map((m) => ({ id: m.id, title: m.title, category: m.category, modified: m.modified })),
+            }, null, 2));
+        }
+        else {
+            console.log(formatWorkingSet(workingSet));
+        }
+    }
+    catch (err) {
+        console.error(`Error: ${err instanceof Error ? err.message : err}`);
+        process.exit(1);
+    }
+    finally {
+        centralDb?.close();
+    }
+});
 program.parse();
 //# sourceMappingURL=cli.js.map