nexarch 0.9.31 → 0.10.1

package/dist/commands/init-agent.js

@@ -1333,7 +1333,7 @@ export async function initAgent(args) {
                 console.log(`   Trust attestation unavailable (${trustAttestation?.reason ?? "unknown"}).`);
             }
         }
-        if (needsIdentityInput) {
+        if (needsIdentityInput && !fromSetup) {
             console.log("\nℹ Additional identity details are still needed to complete agent profile enrichment.");
             console.log(`   Missing: ${identityCapture.missingRequired.join(", ")}`);
             console.log("   In an interactive terminal, rerun 'npx nexarch@latest init-agent' and answer prompts.");

package/dist/commands/init-project.js

@@ -1490,7 +1490,8 @@ export async function initProject(args) {
     // Upsert entities (chunked for progressive feedback)
     const entityChunks = chunkArray(entities, Math.max(1, upsertBatchSize));
     const entitiesResult = {
-        summary: { requested: 0, succeeded: 0, failed: 0 },
+        summary: { requested: 0, succeeded: 0, failed: 0, preserved: 0 },
+        preserved: [],
         errors: [],
     };
     logProgress("upsert.entities.start", `count=${entities.length}, batches=${entityChunks.length}, batchSize=${Math.max(1, upsertBatchSize)}`);
@@ -1511,7 +1512,10 @@ export async function initProject(args) {
         }
         entitiesResult.summary.requested = Number(entitiesResult.summary.requested ?? 0) + Number(chunkResult.summary?.requested ?? chunk.length);
         entitiesResult.summary.succeeded = Number(entitiesResult.summary.succeeded ?? 0) + Number(chunkResult.summary?.succeeded ?? 0);
+        entitiesResult.summary.preserved = Number(entitiesResult.summary.preserved ?? 0) + Number(chunkResult.summary?.preserved ?? 0);
         entitiesResult.summary.failed = Number(entitiesResult.summary.failed ?? 0) + Number(chunkResult.summary?.failed ?? 0);
+        if (chunkResult.preserved?.length)
+            entitiesResult.preserved.push(...chunkResult.preserved);
         if (chunkResult.errors?.length)
             entitiesResult.errors.push(...chunkResult.errors);
         logProgress("upsert.entities.batch.done", `${i + 1}/${entityChunks.length} succeeded=${chunkResult.summary?.succeeded ?? 0}, failed=${chunkResult.summary?.failed ?? 0}`);
@@ -1620,11 +1624,20 @@ export async function initProject(args) {
                 addRelationship: `nexarch add-relationship --from "decision_record:${projectSlug}_<adr_slug>" --to "${projectExternalKey}" --type decides`,
             },
         });
+        const preservedEntities = entitiesResult.preserved ?? [];
         return {
             status: "enrichment_required",
             note: refreshMode
                 ? "Execute ALL pendingSteps. In refresh mode, compare graphState vs scanState to identify gaps — do not blindly remove relationships the scanner missed; the scanner cannot detect platforms, integrations, data assets, or application_functions."
                 : "Execute ALL pendingSteps before reporting the project as registered. Do not pause or ask for confirmation between steps.",
+            ...(refreshMode && preservedEntities.length > 0
+                ? {
+                    preservedEntities: {
+                        note: "These entities already have enriched content and were NOT overwritten by the scan. Review the scan values — if anything has genuinely changed, update with nexarch update-entity.",
+                        entities: preservedEntities,
+                    },
+                }
+                : {}),
             projectEntity: {
                 externalKey: projectExternalKey,
                 entityType: entityTypeOverride,
@@ -1709,11 +1722,19 @@ export async function initProject(args) {
     // This is addressed to the *calling agent* (Claude Code, Codex, etc.) and tells it
     // to act inline in this same session — not to queue enrichment for later.
     function buildEnrichmentDirective() {
+        const preservedEntities = entitiesResult.preserved ?? [];
         const lines = [];
-        lines.push("─── ENRICHMENT REQUIRED ─────────────────────────────────────────────────");
-        lines.push("init-project wrote a skeleton. Complete enrichment below — do not ask the");
-        lines.push("user for permission, do not summarise and pause, just execute the steps.");
-        lines.push("Do NOT report the project as registered until enrichment is done.");
+        if (refreshMode) {
+            lines.push("─── REFRESH REVIEW REQUIRED ──────────────────────────────────────────────");
+            lines.push("update-project refreshed the scan. Review enriched entities and complete any");
+            lines.push("new skeletons below — do not ask the user for permission, just execute.");
+        }
+        else {
+            lines.push("─── ENRICHMENT REQUIRED ─────────────────────────────────────────────────");
+            lines.push("init-project wrote a skeleton. Complete enrichment below — do not ask the");
+            lines.push("user for permission, do not summarise and pause, just execute the steps.");
+            lines.push("Do NOT report the project as registered until enrichment is done.");
+        }
         lines.push("");
         lines.push(`PROJECT : ${projectExternalKey}`);
         lines.push(`DIR     : ${dir}`);
@@ -1759,6 +1780,19 @@ export async function initProject(args) {
             if (unresolvedItems.length > 20)
                 lines.push(`  … and ${unresolvedItems.length - 20} more`);
         }
+        if (refreshMode && preservedEntities.length > 0) {
+            lines.push("");
+            lines.push(`ENRICHED (${preservedEntities.length} — already have descriptions; not overwritten by scan):`);
+            lines.push("  Review each entry. If the scan detected a real change, run update-entity manually.");
+            for (const p of preservedEntities) {
+                lines.push(`  ${p.externalKey ?? "?"}`);
+                lines.push(`    current : name="${p.currentValues?.name ?? ""}" subtype="${p.currentValues?.entitySubtypeCode ?? ""}"`);
+                lines.push(`    scan    : name="${p.scanValues?.name ?? ""}" subtype="${p.scanValues?.entitySubtypeCode ?? ""}"`);
+                if (p.currentValues?.name !== p.scanValues?.name || p.currentValues?.entitySubtypeCode !== p.scanValues?.entitySubtypeCode) {
+                    lines.push(`    ⚠ values differ — review and update if the change is real`);
+                }
+            }
+        }
         lines.push("");
         lines.push("THEN_RUN (execute these steps — do not pause or ask for confirmation):");
         let step = 1;
@@ -1848,7 +1882,8 @@ export async function initProject(args) {
     }
     console.log(`\nDone.`);
     console.log(`  Mode         : ${refreshMode ? "refresh (update-project)" : "init"}`);
-    console.log(`  Entities     : ${output.entities.succeeded ?? 0} written, ${output.entities.failed ?? 0} failed`);
+    const preservedCount = output.entities.preserved ?? 0;
+    console.log(`  Entities     : ${output.entities.succeeded ?? 0} written, ${preservedCount > 0 ? `${preservedCount} preserved (enriched), ` : ""}${output.entities.failed ?? 0} failed`);
     console.log(`  Relationships: ${output.relationships.succeeded ?? 0} written`);
     console.log("  Status       : skeleton created; enrichment pending");
     if (output.metrics.relationshipsSkippedAsDuplicate > 0) {

package/dist/commands/mcp-config.js

@@ -6,6 +6,10 @@ function renderConfigForProfile(profile) {
     if (profile.mergeStrategy === "continue_style") {
         return { mcpServers: [{ name: "nexarch", ...serverBlock }] };
     }
+    if (profile.mergeStrategy === "codex_style") {
+        const args = profile.serverArgs.map((a) => JSON.stringify(a)).join(", ");
+        return `[mcp_servers.nexarch]\ncommand = ${JSON.stringify(profile.serverCommand)}\nargs = [${args}]`;
+    }
     return { mcpServers: { nexarch: serverBlock } };
 }
 export async function mcpConfig(args) {
@@ -43,7 +47,7 @@ If your client requires an MCP server URL instead of command/args, use:
     const config = renderConfigForProfile(profile);
     console.log(`\nUsing integration registry release v${registry.release.version}.`);
     console.log(`\nMCP server config for ${profile.code} (${profile.name}):\n`);
-    console.log(JSON.stringify(config, null, 2));
+    console.log(typeof config === "string" ? config : JSON.stringify(config, null, 2));
     const platformKey = process.platform === "darwin" ? "darwin" : process.platform === "win32" ? "win32" : "linux";
     const locations = profile.osPaths?.[platformKey] ?? [];
     if (locations.length > 0) {

package/dist/commands/setup.js

@@ -67,9 +67,9 @@ export async function setup(args) {
     if (clients.length > 0) {
         const names = clients.map((c) => c.name);
         const listed = names.length === 1 ? names[0] : `${names.slice(0, -1).join(", ")} and ${names[names.length - 1]}`;
-        console.log(`\nSetup complete. Open a new ${listed} session — Nexarch will self-register on startup.`);
+        console.log(`\nSetup complete. Open a new ${listed} session and ask your agent to "register with Nexarch".`);
     }
     else {
-        console.log("\nSetup complete. Once you have configured an MCP client (see above), open a new session — Nexarch will self-register on startup.");
+        console.log('\nSetup complete. Once you have configured an MCP client (see above), open a new session and ask your agent to "register with Nexarch".');
     }
 }

package/dist/lib/clients.js

@@ -60,12 +60,25 @@ function mergeFlatStyle(existing, serverBlock) {
     config.mcpServers = servers;
     return JSON.stringify(config, null, 2);
 }
+function mergeCodexStyle(existing, serverBlock) {
+    const sb = serverBlock;
+    const command = sb.command ?? "npx";
+    const args = (sb.args ?? []).map((a) => JSON.stringify(a)).join(", ");
+    const section = `[mcp_servers.nexarch]\ncommand = ${JSON.stringify(command)}\nargs = [${args}]\n`;
+    const sectionPattern = /\[mcp_servers\.nexarch\][\s\S]*?(?=\n\[|\n*$)/;
+    if (sectionPattern.test(existing)) {
+        return existing.replace(sectionPattern, section.trimEnd());
+    }
+    return existing + (existing.length > 0 && !existing.endsWith("\n") ? "\n" : "") + "\n" + section;
+}
 function mergeForStrategy(strategy) {
     switch (strategy) {
         case "claude_style":
             return mergeClaudeStyle;
         case "continue_style":
             return mergeContinueStyle;
+        case "codex_style":
+            return mergeCodexStyle;
         case "flat_style":
         default:
             return mergeFlatStyle;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nexarch",
-  "version": "0.9.31",
+  "version": "0.10.1",
   "description": "Your architecture workspace for AI delivery.",
   "keywords": [
     "nexarch",