nexarch 0.9.3 → 0.9.5

package/dist/commands/init-agent.js

@@ -59,12 +59,12 @@ async function promptForValue(promptText, required = false) {
         rl.close();
     }
 }
-async function confirmInstructionWrite() {
+async function confirmInstructionWrite(promptText = "Allow nexarch init-agent to write/update AGENTS.md/CLAUDE.md registration instructions? [y/N]: ") {
     if (!process.stdin.isTTY || !process.stdout.isTTY)
         return false;
     const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
     try {
-        const answer = (await rl.question("Allow nexarch init-agent to write/update AGENTS.md/CLAUDE.md registration instructions? [y/N]: ")).trim().toLowerCase();
+        const answer = (await rl.question(promptText)).trim().toLowerCase();
         return answer === "y" || answer === "yes";
     }
     finally {
@@ -1084,20 +1084,25 @@ export async function initAgent(args) {
         catch {
             // non-fatal
         }
+        let existingInstructionTargets = injectAgentConfigs(registry);
+        if (existingInstructionTargets.length === 0) {
+            existingInstructionTargets = injectGenericAgentConfig(registry);
+        }
+        const alreadyConfigured = existingInstructionTargets.length > 0 && existingInstructionTargets.every((r) => r.status === "already_present");
         if (denyInstructionWriteFlag) {
             instructionsWriteAllowed = false;
         }
         else if (allowInstructionWriteFlag) {
             instructionsWriteAllowed = true;
         }
+        else if (alreadyConfigured) {
+            instructionsWriteAllowed = false;
+        }
         else if (!asJson) {
             instructionsWriteAllowed = await confirmInstructionWrite();
         }
         if (instructionsWriteAllowed) {
-            agentConfigResults = injectAgentConfigs(registry);
-            if (agentConfigResults.length === 0) {
-                agentConfigResults = injectGenericAgentConfig(registry);
-            }
+            agentConfigResults = existingInstructionTargets;
             if (agentConfigResults.length > 0) {
                 trustAttestationAttempted = true;
                 trustAttestation = await requestTrustAttestation(agentId);
@@ -1116,6 +1121,9 @@ export async function initAgent(args) {
                 }
             }
         }
+        else if (alreadyConfigured) {
+            agentConfigResults = existingInstructionTargets;
+        }
     }
     checks.push({
         name: "agent.registration",
@@ -1132,29 +1140,34 @@ export async function initAgent(args) {
                 ? `awaiting identity input (${identityCapture.missingRequired.join(", ")})`
                 : identityCapture.detail,
     });
+    const instructionsAlreadyConfigured = agentConfigResults.length > 0 && agentConfigResults.every((r) => r.status === "already_present");
     checks.push({
         name: "agent.instructions.injection",
         ok: !registration.ok || !instructionsWriteAllowed || agentConfigResults.length > 0,
         detail: !registration.ok
             ? "skipped (registration failed)"
-            : !instructionsWriteAllowed
-                ? "skipped (consent not granted)"
-                : agentConfigResults.length > 0
-                    ? `updated ${agentConfigResults.length} instruction target file(s)`
-                    : "no runtime instruction target matched this repository (non-fatal; create AGENTS.md/CLAUDE.md or configure a generic target)",
+            : instructionsAlreadyConfigured
+                ? "already configured (no write needed)"
+                : !instructionsWriteAllowed
+                    ? "skipped (consent not granted)"
+                    : agentConfigResults.length > 0
+                        ? `updated ${agentConfigResults.length} instruction target file(s)`
+                        : "no runtime instruction target matched this repository (non-fatal; create AGENTS.md/CLAUDE.md or configure a generic target)",
     });
     checks.push({
         name: "agent.trust.attestation",
         ok: !registration.ok || !instructionsWriteAllowed || !trustAttestationAttempted || Boolean(trustAttestation?.ok),
         detail: !registration.ok
             ? "skipped (registration failed)"
-            : !instructionsWriteAllowed
-                ? "skipped (consent not granted)"
-                : !trustAttestationAttempted
-                    ? "skipped (no instruction target written)"
-                    : trustAttestation?.ok
-                        ? "minted and injected into instruction file(s)"
-                        : `unavailable (${trustAttestation?.reason ?? "unknown"})`,
+            : instructionsAlreadyConfigured && !instructionsWriteAllowed
+                ? "skipped (already configured)"
+                : !instructionsWriteAllowed
+                    ? "skipped (consent not granted)"
+                    : !trustAttestationAttempted
+                        ? "skipped (no instruction target written)"
+                        : trustAttestation?.ok
+                            ? "minted and injected into instruction file(s)"
+                            : `unavailable (${trustAttestation?.reason ?? "unknown"})`,
     });
     checks.push({
         name: "technology.components",

package/dist/commands/init-project.js

@@ -28,6 +28,14 @@ function formatMs(ms) {
         return `${ms}ms`;
     return `${(ms / 1000).toFixed(2)}s`;
 }
+function chunkArray(items, size) {
+    if (size <= 0)
+        return [items];
+    const chunks = [];
+    for (let i = 0; i < items.length; i += size)
+        chunks.push(items.slice(i, i + size));
+    return chunks;
+}
 function slugify(name) {
     return name.toLowerCase().replace(/[^a-z0-9]+/g, "_").replace(/^_+|_+$/g, "");
 }
@@ -956,12 +964,34 @@ async function promptApplicationChoice(matches, allApps, suggested) {
 export async function initProject(args) {
     const asJson = parseFlag(args, "--json");
     const dryRun = parseFlag(args, "--dry-run");
+    const profileEnabled = parseFlag(args, "--profile");
     const commandStartedAt = Date.now();
+    const profile = {
+        enabled: profileEnabled,
+        startedAt: new Date(commandStartedAt).toISOString(),
+        events: [],
+        mcpCalls: [],
+        upsertBatches: {
+            entities: [],
+            relationships: [],
+        },
+    };
     const logProgress = (phase, details) => {
-        const elapsed = formatMs(Date.now() - commandStartedAt);
+        const atMs = Date.now() - commandStartedAt;
+        if (profileEnabled)
+            profile.events.push({ phase, atMs, details });
+        const elapsed = formatMs(atMs);
         const line = details ? `[init-project +${elapsed}] ${phase} — ${details}` : `[init-project +${elapsed}] ${phase}`;
         process.stderr.write(`${line}\n`);
     };
+    const callMcpProfiled = async (toolName, input, meta) => {
+        const startedAt = Date.now();
+        const result = await callMcpTool(toolName, input, mcpOpts);
+        if (profileEnabled) {
+            profile.mcpCalls.push({ tool: toolName, durationMs: Date.now() - startedAt, meta });
+        }
+        return result;
+    };
     const dirArg = parseOptionValue(args, "--dir") ?? process.cwd();
     const dir = resolvePath(dirArg);
     const nameOverride = parseOptionValue(args, "--name");
@@ -973,6 +1003,7 @@ export async function initProject(args) {
     const forceCreateApplication = parseFlag(args, "--create-application");
     const autoMapApplication = parseFlag(args, "--auto-map-application");
     const nonInteractive = parseFlag(args, "--non-interactive");
+    const upsertBatchSize = Number(parseOptionValue(args, "--batch-size") ?? "10") || 10;
     const creds = requireCredentials();
     const mcpOpts = { companyId: creds.companyId };
     if (!asJson)
@@ -1021,7 +1052,7 @@ export async function initProject(args) {
     for (let i = 0; i < detectedNames.length; i += BATCH_SIZE) {
         const batch = detectedNames.slice(i, i + BATCH_SIZE);
         logProgress("resolve.batch", `${Math.floor(i / BATCH_SIZE) + 1}/${Math.ceil(detectedNames.length / BATCH_SIZE)} size=${batch.length}`);
-        const raw = await callMcpTool("nexarch_resolve_reference", { names: batch, companyId: creds.companyId }, mcpOpts);
+        const raw = await callMcpProfiled("nexarch_resolve_reference", { names: batch, companyId: creds.companyId }, { batchSize: batch.length });
         const data = parseToolText(raw);
         allResolveResults.push(...data.results);
     }
@@ -1061,7 +1092,7 @@ export async function initProject(args) {
         return;
     }
     logProgress("preflight.onboarding.check");
-    const onboardingRaw = await callMcpTool("nexarch_get_company_onboarding", {}, mcpOpts);
+    const onboardingRaw = await callMcpProfiled("nexarch_get_company_onboarding", {});
     const onboarding = parseToolText(onboardingRaw);
     if (onboarding.isComplete !== true) {
         const message = "Company onboarding is incomplete. Complete onboarding before running init-project.";
@@ -1074,7 +1105,7 @@ export async function initProject(args) {
     }
     // Policy bootstrap
     logProgress("preflight.policies.check");
-    const policiesRaw = await callMcpTool("nexarch_get_applied_policies", {}, mcpOpts);
+    const policiesRaw = await callMcpProfiled("nexarch_get_applied_policies", {});
     const policies = parseToolText(policiesRaw);
     const policyBundleHash = policies.policyBundleHash ?? null;
     if (!policyBundleHash) {
@@ -1099,7 +1130,7 @@ export async function initProject(args) {
                 console.log(`\nUsing --application-ref target: ${projectExternalKey}`);
         }
         else {
-            const appsRaw = await callMcpTool("nexarch_list_entities", { entityTypeCode: "application", status: "active", limit: 500, companyId: creds.companyId }, mcpOpts);
+            const appsRaw = await callMcpProfiled("nexarch_list_entities", { entityTypeCode: "application", status: "active", limit: 500, companyId: creds.companyId }, { entityTypeCode: "application", limit: 500 });
             const appsData = parseToolText(appsRaw);
             const apps = (appsData.entities ?? []).filter((e) => (e.entityRef ?? e.externalKey));
             if (apps.length > 0) {
@@ -1116,18 +1147,40 @@ export async function initProject(args) {
                         console.log(`\nAuto-mapped to existing application: ${suggested.name} (${projectExternalKey})`);
                 }
                 else if (!interactiveAllowed) {
-                    if (highConfidence) {
-                        projectExternalKey = suggested.entityRef;
+                    const message = "Application mapping requires explicit choice in non-interactive mode. Pass --application-ref <entityRef> or --create-application (or run interactively).";
+                    const existingApplications = apps.slice(0, 25).map((a) => ({
+                        entityRef: a.entityRef ?? a.externalKey,
+                        name: a.name,
+                        entityTypeCode: a.entityTypeCode,
+                    }));
+                    if (asJson) {
+                        process.stdout.write(`${JSON.stringify({
+                            ok: true,
+                            status: "input_required",
+                            code: "APPLICATION_MAPPING_REQUIRED",
+                            message,
+                            suggested: suggested ?? null,
+                            candidates: matches.slice(0, 10),
+                            existingApplications,
+                            requiredInput: {
+                                applicationRefOption: "--application-ref <entityRef>",
+                                createOption: "--create-application",
+                            },
+                        }, null, 2)}\n`);
+                        return;
+                    }
+                    console.log("\nInput required before continuing:");
+                    console.log(`  ${message}`);
+                    if (suggested) {
+                        console.log(`  Suggested: ${suggested.name} (${suggested.entityRef}) score=${suggested.score.toFixed(2)}`);
                     }
-                    else if (autoMapApplication) {
-                        const message = "Ambiguous application mapping in non-interactive mode. Pass --application-ref or --create-application.";
-                        if (asJson) {
-                            process.stdout.write(`${JSON.stringify({ ok: false, error: "APPLICATION_MAPPING_AMBIGUOUS", message, candidates: matches.slice(0, 5) }, null, 2)}\n`);
-                            process.exitCode = 1;
-                            return;
+                    if (existingApplications.length > 0) {
+                        console.log("  Existing applications:");
+                        for (const app of existingApplications) {
+                            console.log(`    - ${app.name} (${app.entityRef})`);
                         }
-                        throw new Error(message);
                     }
+                    return;
                 }
                 else {
                     const chosen = await promptApplicationChoice(matches, apps, highConfidence ? suggested : null);
@@ -1290,7 +1343,7 @@ export async function initProject(args) {
     // Company org is accountable_for the top-level project entity
     let orgExternalKey = `organisation:${normalizeToken(creds.companyId)}`;
     try {
-        const orgRaw = await callMcpTool("nexarch_list_entities", { entityTypeCode: "organisation", status: "active", limit: 1, companyId: creds.companyId }, mcpOpts);
+        const orgRaw = await callMcpProfiled("nexarch_list_entities", { entityTypeCode: "organisation", status: "active", limit: 1, companyId: creds.companyId }, { entityTypeCode: "organisation", limit: 1 });
         const orgData = parseToolText(orgRaw);
         const org = (orgData.entities ?? [])[0];
         if (org?.entityRef || org?.externalKey)
@@ -1312,17 +1365,64 @@ export async function initProject(args) {
     }
     if (!asJson)
         console.log(`\nWriting to graph…`);
-    // Upsert entities
-    logProgress("upsert.entities.start", `count=${entities.length}`);
-    const entitiesRaw = await callMcpTool("nexarch_upsert_entities", { entities, agentContext, policyContext }, mcpOpts);
-    const entitiesResult = parseToolText(entitiesRaw);
+    // Upsert entities (chunked for progressive feedback)
+    const entityChunks = chunkArray(entities, Math.max(1, upsertBatchSize));
+    const entitiesResult = {
+        summary: { requested: 0, succeeded: 0, failed: 0 },
+        errors: [],
+    };
+    logProgress("upsert.entities.start", `count=${entities.length}, batches=${entityChunks.length}, batchSize=${Math.max(1, upsertBatchSize)}`);
+    for (let i = 0; i < entityChunks.length; i += 1) {
+        const chunk = entityChunks[i];
+        logProgress("upsert.entities.batch.start", `${i + 1}/${entityChunks.length} size=${chunk.length}`);
+        const entityBatchStartedAt = Date.now();
+        const entitiesRaw = await callMcpProfiled("nexarch_upsert_entities", { entities: chunk, agentContext, policyContext }, { batchIndex: i + 1, totalBatches: entityChunks.length, batchSize: chunk.length });
+        const chunkResult = parseToolText(entitiesRaw);
+        if (profileEnabled) {
+            profile.upsertBatches.entities.push({
+                index: i + 1,
+                size: chunk.length,
+                durationMs: Date.now() - entityBatchStartedAt,
+                succeeded: Number(chunkResult.summary?.succeeded ?? 0),
+                failed: Number(chunkResult.summary?.failed ?? 0),
+            });
+        }
+        entitiesResult.summary.requested = Number(entitiesResult.summary.requested ?? 0) + Number(chunkResult.summary?.requested ?? chunk.length);
+        entitiesResult.summary.succeeded = Number(entitiesResult.summary.succeeded ?? 0) + Number(chunkResult.summary?.succeeded ?? 0);
+        entitiesResult.summary.failed = Number(entitiesResult.summary.failed ?? 0) + Number(chunkResult.summary?.failed ?? 0);
+        if (chunkResult.errors?.length)
+            entitiesResult.errors.push(...chunkResult.errors);
+        logProgress("upsert.entities.batch.done", `${i + 1}/${entityChunks.length} succeeded=${chunkResult.summary?.succeeded ?? 0}, failed=${chunkResult.summary?.failed ?? 0}`);
+    }
     logProgress("upsert.entities.done", `succeeded=${entitiesResult.summary?.succeeded ?? 0}, failed=${entitiesResult.summary?.failed ?? 0}`);
-    // Upsert relationships
+    // Upsert relationships (chunked)
     let relsResult = null;
     if (relationships.length > 0) {
-        logProgress("upsert.relationships.start", `count=${relationships.length}`);
-        const relsRaw = await callMcpTool("nexarch_upsert_relationships", { relationships, agentContext, policyContext }, mcpOpts);
-        relsResult = parseToolText(relsRaw);
+        const relationshipChunks = chunkArray(relationships, Math.max(1, upsertBatchSize));
+        relsResult = { summary: { requested: 0, succeeded: 0, failed: 0 }, errors: [] };
+        logProgress("upsert.relationships.start", `count=${relationships.length}, batches=${relationshipChunks.length}, batchSize=${Math.max(1, upsertBatchSize)}`);
+        for (let i = 0; i < relationshipChunks.length; i += 1) {
+            const chunk = relationshipChunks[i];
+            logProgress("upsert.relationships.batch.start", `${i + 1}/${relationshipChunks.length} size=${chunk.length}`);
+            const relBatchStartedAt = Date.now();
+            const relsRaw = await callMcpProfiled("nexarch_upsert_relationships", { relationships: chunk, agentContext, policyContext }, { batchIndex: i + 1, totalBatches: relationshipChunks.length, batchSize: chunk.length });
+            const chunkResult = parseToolText(relsRaw);
+            if (profileEnabled) {
+                profile.upsertBatches.relationships.push({
+                    index: i + 1,
+                    size: chunk.length,
+                    durationMs: Date.now() - relBatchStartedAt,
+                    succeeded: Number(chunkResult.summary?.succeeded ?? 0),
+                    failed: Number(chunkResult.summary?.failed ?? 0),
+                });
+            }
+            relsResult.summary.requested = Number(relsResult.summary.requested ?? 0) + Number(chunkResult.summary?.requested ?? chunk.length);
+            relsResult.summary.succeeded = Number(relsResult.summary.succeeded ?? 0) + Number(chunkResult.summary?.succeeded ?? 0);
+            relsResult.summary.failed = Number(relsResult.summary.failed ?? 0) + Number(chunkResult.summary?.failed ?? 0);
+            if (chunkResult.errors?.length)
+                relsResult.errors.push(...chunkResult.errors);
+            logProgress("upsert.relationships.batch.done", `${i + 1}/${relationshipChunks.length} succeeded=${chunkResult.summary?.succeeded ?? 0}, failed=${chunkResult.summary?.failed ?? 0}`);
+        }
         logProgress("upsert.relationships.done", `succeeded=${relsResult.summary?.succeeded ?? 0}, failed=${relsResult.summary?.failed ?? 0}`);
     }
     // Build structured enrichment task (included in JSON output and printed in human mode)
@@ -1573,6 +1673,15 @@ ${subPkgSection}${adrSection}${gapCheckSection}`;
         entityErrors: entitiesResult.errors ?? [],
         relationshipErrors: relsResult?.errors ?? [],
         enrichmentTask,
+        profile: profileEnabled
+            ? {
+                startedAt: profile.startedAt,
+                totalDurationMs: Date.now() - commandStartedAt,
+                events: profile.events,
+                mcpCalls: profile.mcpCalls,
+                upsertBatches: profile.upsertBatches,
+            }
+            : undefined,
     };
     if (asJson) {
         logProgress("complete", `ok=${output.ok}`);

package/dist/index.js

@@ -94,6 +94,8 @@ Usage:
                                --create-application  force new application entity
                                --auto-map-application  auto-map only when high confidence
                                --non-interactive  fail on ambiguous mapping
+                               --batch-size <n>  upsert batch size (default: 10)
+                               --profile  include timing/profile data in JSON output
                                --dry-run  preview without writing
                                --json
   nexarch update-entity

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nexarch",
-  "version": "0.9.3",
+  "version": "0.9.5",
   "description": "Your architecture workspace for AI delivery.",
   "keywords": [
     "nexarch",