npm - @pennixrv/trellis - Versions diffs - 0.7.0-beta.35 → 0.7.0-beta.39 - Mend

@pennixrv/trellis 0.7.0-beta.35 → 0.7.0-beta.39

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (65) hide show

package/dist/commands/channel/supervisor/stdout.js CHANGED Viewed

@@ -159,7 +159,7 @@ export async function applyParseResult(channelName, workerName, result, child, s
         // racing `child.on("exit") → finalizeOnExit` can't see
         // `terminalEmitted=false` and synthesise a duplicate fallback while
         // we're in the middle of writing the real terminal event.
-        if (ev.kind === "done" || ev.kind === "error") {
+        if (ev.kind === "done") {
             shutdown.markTerminalEmitted();
         }
         await appendEvent(channelName, {
@@ -222,16 +222,17 @@ export function startStdoutPump(args) {
     const drained = pumpStdout(child.stdout, async (line) => {
         if (processLines && !(await processLines))
             return;
-        log.write(line + "\n");
         const result = adapter.parseLine(line, adapterCtx);
         await applyParseResult(channelName, workerName, result, child, shutdown, turnTracker, project, onDone);
     }, async (err) => {
-        log.write(`[supervisor] stdout line handler failed: ${err.message}\n`);
+        shutdown.claim("crash");
+        log.write("[supervisor] stdout line handler failed (detail in sanitized error event)\n");
         await appendEvent(channelName, {
             kind: "error",
             by: `supervisor:${workerName}`,
             message: `stdout pipeline error: ${err.message}`,
         }, project).catch(() => undefined);
+        await shutdown.request("SIGTERM", "crash");
     }, signal);
     return processLines
         ? Promise.all([drained, processLines]).then(() => undefined)

package/dist/commands/channel/supervisor/stdout.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/commands/channel/supervisor/warning.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"warning.d.ts","sourceRoot":"","sources":["../../../../src/commands/channel/supervisor/warning.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAIH,gFAAgF;AAChF,eAAO,MAAM,uCAAuC,QAAa,CAAC;AAElE,MAAM,WAAW,uBAAuB;IACtC,cAAc,IAAI,OAAO,CAAC;IAC1B,gBAAgB,IAAI,OAAO,CAAC;CAC7B;AAED,MAAM,WAAW,oCAAoC;IACnD,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,wEAAwE;IACxE,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,uBAAuB,CAAC;IAClC,gFAAgF;IAChF,aAAa,EAAE,MAAM,OAAO,CAAC;IAC7B,GAAG,EAAE;QAAE,KAAK,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,IAAI,CAAA;KAAE,CAAC;IACvC,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,gCAAgC,CAC9C,IAAI,EAAE,oCAAoC,GACzC,MAAM,IAAI,~~CAuDZ~~"}
1	+ {"version":3,"file":"warning.d.ts","sourceRoot":"","sources":["../../../../src/commands/channel/supervisor/warning.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAIH,gFAAgF;AAChF,eAAO,MAAM,uCAAuC,QAAa,CAAC;AAElE,MAAM,WAAW,uBAAuB;IACtC,cAAc,IAAI,OAAO,CAAC;IAC1B,gBAAgB,IAAI,OAAO,CAAC;CAC7B;AAED,MAAM,WAAW,oCAAoC;IACnD,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,wEAAwE;IACxE,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,uBAAuB,CAAC;IAClC,gFAAgF;IAChF,aAAa,EAAE,MAAM,OAAO,CAAC;IAC7B,GAAG,EAAE;QAAE,KAAK,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,IAAI,CAAA;KAAE,CAAC;IACvC,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,gCAAgC,CAC9C,IAAI,EAAE,oCAAoC,GACzC,MAAM,IAAI,CAsDZ"}

package/dist/commands/channel/supervisor/warning.js CHANGED Viewed

@@ -60,9 +60,8 @@ export function scheduleSupervisorTimeoutWarning(args) {
                     remaining_ms: remaining,
                 }, args.project);
             }
-            catch (err) {
-                const msg = err instanceof Error ? err.message : String(err);
-                log.write(`[supervisor] warning append failed: ${msg}\n`);
+            catch {
+                log.write("[supervisor] warning append failed\n");
             }
         })();
     };

package/dist/commands/channel/supervisor/warning.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/commands/channel/supervisor.d.ts CHANGED Viewed

@@ -28,6 +28,8 @@ export interface SupervisorConfig {
     systemPrompt: string;
     /** Extra env vars (TRELLIS_HOOKS=0 etc. are added automatically). */
     env?: Record<string, string>;
+    /** Names from an explicitly trusted agent env_file; values stay in process env. */
+    roleEnvKeys?: string[];
     /** Optional model override. */
     model?: string;
     reasoningEffort?: ReasoningEffort;
@@ -66,7 +68,7 @@ export interface SupervisorConfig {
     inboxPolicy?: InboxPolicy;
 }
 /** Merge parent, role, and runtime settings in increasing precedence. */
-export declare function buildWorkerEnv(config: Pick<SupervisorConfig, "provider" | "agent" | "env">, parent: NodeJS.ProcessEnv, runtime: NodeJS.ProcessEnv): NodeJS.ProcessEnv;
+export declare function buildWorkerEnv(config: Pick<SupervisorConfig, "provider" | "agent" | "env" | "roleEnvKeys">, parent: NodeJS.ProcessEnv, runtime: NodeJS.ProcessEnv): NodeJS.ProcessEnv;
 interface ResolvedProviderPath {
     command: string;
     prefixArgs: string[];

package/dist/commands/channel/supervisor.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/commands/channel/supervisor.js CHANGED Viewed

@@ -14,10 +14,11 @@
 import { spawn } from "node:child_process";
 import fs from "node:fs";
 import path from "node:path";
-import { DEFAULT_INBOX_POLICY, } from "@pennixrv/trellis-core/channel";
+import { DEFAULT_INBOX_POLICY, redactDiagnostic, } from "@pennixrv/trellis-core/channel";
 import { shouldUseSystemPromptFile } from "./adapters/claude.js";
 import { getAdapter } from "./adapters/index.js";
 import { appendEvent } from "./store/events.js";
+import { readProcessIdentity } from "./process-identity.js";
 import { workerFile } from "./store/paths.js";
 import { scheduleSupervisorIdleTimer } from "./supervisor/idle.js";
 import { runInboxWatcher } from "./supervisor/inbox.js";
@@ -27,7 +28,43 @@ import { TurnTracker } from "./supervisor/turns.js";
 import { scheduleSupervisorTimeoutWarning } from "./supervisor/warning.js";
 /** Merge parent, role, and runtime settings in increasing precedence. */
 export function buildWorkerEnv(config, parent, runtime) {
-    return { ...parent, ...config.env, ...runtime };
+    const common = new Set([
+        "PATH",
+        "HOME",
+        "USER",
+        "LOGNAME",
+        "SHELL",
+        "TMPDIR",
+        "TMP",
+        "TEMP",
+        "LANG",
+        "LC_ALL",
+        "LC_CTYPE",
+        "TERM",
+        "COLORTERM",
+        "NO_COLOR",
+        "XDG_CONFIG_HOME",
+        "XDG_CACHE_HOME",
+        "XDG_DATA_HOME",
+        "SSL_CERT_FILE",
+        "SSL_CERT_DIR",
+        "HTTP_PROXY",
+        "HTTPS_PROXY",
+        "ALL_PROXY",
+        "NO_PROXY",
+    ]);
+    const providerPrefix = config.provider === "claude"
+        ? /^(?:ANTHROPIC|CLAUDE)_/
+        : /^(?:OPENAI|CODEX|AZURE_OPENAI)_/;
+    const explicit = new Set(config.roleEnvKeys ?? []);
+    const selected = {};
+    for (const [key, value] of Object.entries(parent)) {
+        if (value !== undefined &&
+            (common.has(key) || providerPrefix.test(key) || explicit.has(key))) {
+            selected[key] = value;
+        }
+    }
+    return { ...selected, ...config.env, ...runtime };
 }
 const SHUTDOWN_GRACE_MS = 3000;
 /**
@@ -143,13 +180,9 @@ export async function runSupervisor(channelName, workerName, configPath) {
         TRELLIS_CHANNEL_AS: workerName,
     });
     const logPath = workerFile(channelName, workerName, "log", project);
-    const log = fs.createWriteStream(logPath);
+    const log = fs.createWriteStream(logPath, { mode: 0o600 });
     const resolvedProvider = resolveProviderPath(adapter.provider, config.cwd);
-    const resolvedProviderDisplay = [
-        resolvedProvider.command,
-        ...resolvedProvider.prefixArgs,
-    ].join(" ");
-    log.write(`[supervisor] starting ${adapter.provider} (resolved: ${resolvedProviderDisplay}) ${args.join(" ")}\n`);
+    log.write(`[supervisor] starting ${adapter.provider}\n`);
     const child = spawn(resolvedProvider.command, [...resolvedProvider.prefixArgs, ...args], {
         cwd: config.cwd,
         env,
@@ -218,7 +251,7 @@ export async function runSupervisor(channelName, workerName, configPath) {
     // lines. Node fires `error` on next tick when spawn fails (ENOENT etc.),
     // and if no listener is attached by then the supervisor dies with an
     // unhandled error and leaves a stale .pid behind.
-    child.stderr.on("data", (b) => log.write(b));
+    child.stderr.on("data", (b) => log.write(`[supervisor] worker stderr: ${b.length} bytes (content omitted)\n`));
     child.once("spawn", () => {
         settleSpawn();
     });
@@ -229,7 +262,7 @@ export async function runSupervisor(channelName, workerName, configPath) {
         // duplicate error events.
         if (spawnFailed || shutdown.isShuttingDown())
             return;
-        log.write(`[supervisor] worker error: ${err.message}\n`);
+        log.write(redactDiagnostic(`[supervisor] worker error: ${err.message}\n`));
         if (!child.pid) {
             // Pre-spawn failure (ENOENT / EACCES): emit ONE `error` event,
             // skip the misleading `spawned{pid:undefined}`, clean up, and exit
@@ -299,7 +332,12 @@ export async function runSupervisor(channelName, workerName, configPath) {
     // into `shutdown.request` instead of using Node's default behaviour
     // (which would orphan the child and skip the `killed` event).
     process.on("SIGTERM", () => {
-        void shutdown.request("SIGTERM", readExternalShutdownReason(channelName, workerName, project));
+        const reason = readExternalShutdownReason(channelName, workerName, project);
+        if (reason === "idle-timeout") {
+            idleTimerRef.current?.expireIfIdle();
+            return;
+        }
+        void shutdown.request("SIGTERM", reason);
     });
     process.on("SIGINT", () => void shutdown.request("SIGINT", "explicit-kill"));
     // SIGHUP arrives when the parent terminal closes — without this
@@ -325,6 +363,11 @@ export async function runSupervisor(channelName, workerName, configPath) {
     }
     try {
         fs.writeFileSync(workerFile(channelName, workerName, "worker-pid", project), String(child.pid));
+        const childIdentity = child.pid
+            ? readProcessIdentity(child.pid)
+            : undefined;
+        if (childIdentity)
+            fs.writeFileSync(workerFile(channelName, workerName, "worker-identity", project), childIdentity, { mode: 0o600 });
         await appendEvent(channelName, {
             kind: "spawned",
             by: config.spawnedBy ?? "main",
@@ -411,6 +454,9 @@ export async function runSupervisor(channelName, workerName, configPath) {
         signal: inboxAbort.signal,
         inboxPolicy: config.inboxPolicy ?? DEFAULT_INBOX_POLICY,
         turnTracker,
+    }).catch(async () => {
+        inboxAbort.abort();
+        await shutdown.request("SIGTERM", "crash");
     });
     // ── adapter handshake (no initial user prompt) ──
     if (adapter.handshake) {
@@ -419,7 +465,7 @@ export async function runSupervisor(channelName, workerName, configPath) {
         }
         catch (err) {
             const msg = err instanceof Error ? err.message : String(err);
-            log.write(`[supervisor] adapter handshake failed: ${msg}\n`);
+            log.write(redactDiagnostic(`[supervisor] adapter handshake failed: ${msg}\n`));
             // Codex #4 fix: emit an `error` event with the handshake message
             // BEFORE requesting shutdown — otherwise the channel only sees a
             // `killed{reason:"crash"}` with no detail on what went wrong.
@@ -455,6 +501,7 @@ async function cleanup(channelName, workerName) {
     for (const suffix of [
         "pid",
         "worker-pid",
+        "worker-identity",
         "config",
         "system-prompt.md",
         "spawnlock",
@@ -489,7 +536,10 @@ function readConfig(p) {
 export function writeSupervisorConfig(channelName, workerName, config, project) {
     const p = workerFile(channelName, workerName, "config", project);
     fs.mkdirSync(path.dirname(p), { recursive: true });
-    fs.writeFileSync(p, JSON.stringify(config, null, 2), "utf-8");
+    fs.writeFileSync(p, JSON.stringify(config, null, 2), {
+        encoding: "utf-8",
+        mode: 0o600,
+    });
     return p;
 }
 //# sourceMappingURL=supervisor.js.map

package/dist/commands/channel/supervisor.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/commands/update.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/commands/update.js CHANGED Viewed

@@ -28,7 +28,7 @@ import { pruneOrphanManifestKeys } from "../utils/manifest-prune.js";
 import { fetchRegistrySpecTemplates, collectDirectoryFiles, removeDirectory, parseRegistrySource, probeRegistryIndex, downloadTemplateById, } from "../utils/template-fetcher.js";
 import { loadSpecRegistryConfig } from "../utils/registry-config.js";
 import { cleanupEmptyDirs, getManagedMarkdownBlock, mergeManagedMarkdownBlock, TRELLIS_BLOCK_END, TRELLIS_BLOCK_START, } from "../utils/managed-paths.js";
-import { loadWorkflowProvenance, workflowProvenanceMismatches, } from "../utils/workflow-provenance.js";
+import { loadWorkflowProvenance, writeWorkflowProvenance, workflowProvenanceMismatches, } from "../utils/workflow-provenance.js";
 import { NATIVE_WORKFLOW_ID, resolveWorkflowTemplate, } from "../utils/workflow-resolver.js";
 export { cleanupEmptyDirs, TRELLIS_BLOCK_END, TRELLIS_BLOCK_START, } from "../utils/managed-paths.js";
 const CLAUDE_SETTINGS_PATH = ".claude/settings.json";
@@ -39,73 +39,6 @@ const LEGACY_UNTRACKED_AGENTS_MD_BLOCK_HASHES = new Set([
     // false "modified by you" conflict.
     "c1f511b1cfc1902f2147da159f09cc51f380b0c9e341cdb3ac5dea5233f3e307",
 ]);
-const CODEX_WORKFLOW_STATE_HOOK_PATH = ".codex/hooks/inject-workflow-state.py";
-const LEGACY_PENNIX_CODEX_DISPATCH_SIGNATURES = [
-    "def _resolve_codex_dispatch_mode(config: dict, repo_root: Path | None = None) -> str:",
-    "from common.config import get_workflow_dispatch_mode",
-    "return get_workflow_dispatch_mode(root, config=config)",
-];
-const LEGACY_PENNIX_ACTIVE_TASK_GUARD = "    active = _resolve_active_task(root, input_data)\n" +
-    "    if not active.task_path:\n" +
-    "        return None";
-const PENNIX_AMBIGUITY_PROJECTION = "    active = _resolve_active_task(root, input_data)\n" +
-    '    if active.source_type == "unbound_ambiguous":\n' +
-    '        candidates = ", ".join(active.candidate_paths)\n' +
-    '        return candidates, "unbound_ambiguous", active.source\n' +
-    "    if not active.task_path:\n" +
-    "        return None";
-const LEGACY_PENNIX_BREADCRUMB_HEADER = '    header = f"Status: {status}" if task_id is None else f"Task: {task_id} ({status})"';
-const PENNIX_AMBIGUITY_BREADCRUMB_HEADER = '    if status == "unbound_ambiguous":\n' +
-    '        header = f"Status: {status}\\nCandidates: {task_id}"\n' +
-    "    else:\n" +
-    '        header = f"Status: {status}" if task_id is None else f"Task: {task_id} ({status})"';
-/**
- * Preserve the historical Pennix Codex hook while adding the one projection
- * it predates. This is intentionally stricter than hash tracking: the Hook
- * carried a Pennix-specific dispatch resolver, so pristine installations were
- * correctly classified as locally modified and never received issue #180.
- */
-function migrateLegacyPennixCodexWorkflowHook(relativePath, existingContent) {
-    if (relativePath !== CODEX_WORKFLOW_STATE_HOOK_PATH ||
-        !LEGACY_PENNIX_CODEX_DISPATCH_SIGNATURES.every((signature) => existingContent.includes(signature))) {
-        return null;
-    }
-    const hasProjection = existingContent.includes(PENNIX_AMBIGUITY_PROJECTION);
-    const hasHeader = existingContent.includes(PENNIX_AMBIGUITY_BREADCRUMB_HEADER);
-    if (hasProjection && hasHeader) {
-        return { content: existingContent, needsUpdate: false };
-    }
-    if ((!hasProjection &&
-        !existingContent.includes(LEGACY_PENNIX_ACTIVE_TASK_GUARD)) ||
-        (!hasHeader && !existingContent.includes(LEGACY_PENNIX_BREADCRUMB_HEADER))) {
-        return null;
-    }
-    return {
-        content: existingContent
-            .replace(LEGACY_PENNIX_ACTIVE_TASK_GUARD, PENNIX_AMBIGUITY_PROJECTION)
-            .replace(LEGACY_PENNIX_BREADCRUMB_HEADER, PENNIX_AMBIGUITY_BREADCRUMB_HEADER),
-        needsUpdate: !hasProjection || !hasHeader,
-    };
-}
-/** Keep recognized Pennix Hook customizations in the desired template map. */
-function preserveLegacyPennixCodexWorkflowHook(cwd, templates) {
-    if (!templates.has(CODEX_WORKFLOW_STATE_HOOK_PATH)) {
-        return;
-    }
-    const hookPath = path.join(cwd, CODEX_WORKFLOW_STATE_HOOK_PATH);
-    if (!fs.existsSync(hookPath)) {
-        return;
-    }
-    try {
-        const migration = migrateLegacyPennixCodexWorkflowHook(CODEX_WORKFLOW_STATE_HOOK_PATH, fs.readFileSync(hookPath, "utf-8"));
-        if (migration) {
-            templates.set(CODEX_WORKFLOW_STATE_HOOK_PATH, migration.content);
-        }
-    }
-    catch {
-        // The normal conflict path reports unreadable or concurrently changed files.
-    }
-}
 // Paths that should never be touched (true user data)
 // spec/ is user-customized content created during init; update should never modify it
 const PROTECTED_PATHS = [
@@ -161,6 +94,9 @@ function isKnownUntrackedTemplate(relativePath, existingContent) {
     if (relativePath !== FILE_NAMES.AGENTS) {
         return false;
     }
+    if (countOccurrences(existingContent, TRELLIS_BLOCK_START) !== 1 ||
+        countOccurrences(existingContent, TRELLIS_BLOCK_END) !== 1)
+        return false;
     const managedBlock = getTrellisManagedBlock(existingContent);
     if (!managedBlock) {
         return false;
@@ -700,7 +636,6 @@ bypassUpdateSkip = false) {
     if (platforms.has("codex")) {
         preserveCodexAgentModelKeys(cwd, files);
         preserveCodexProjectConfig(cwd, files);
-        preserveLegacyPennixCodexWorkflowHook(cwd, files);
     }
     preserveExistingClaudeStatusLine(cwd, files);
     if (platforms.has("claude-code") && isClaudeStatuslineManaged(cwd, hashes)) {
@@ -745,7 +680,14 @@ async function resolveWorkflowUpdateTemplate(cwd, hashes) {
             ? provenance.registry
             : undefined,
     });
-    const mismatches = workflowProvenanceMismatches(provenance, template);
+    const nativeVersionTransition = template.id === NATIVE_WORKFLOW_ID &&
+        template.source === "bundled" &&
+        provenance.ref !== template.ref &&
+        compareVersions(provenance.ref, template.ref) !== null;
+    const mismatches = workflowProvenanceMismatches(provenance, template).filter((mismatch) => !(nativeVersionTransition &&
+        (mismatch === "ref" ||
+            (mismatch === "template integrity" &&
+                hashes[PATHS.WORKFLOW_GUIDE_FILE] === provenance.content_sha256))));
     if (mismatches.length > 0) {
         throw new Error(`Workflow provenance verification failed: ${mismatches.join(", ")}.`);
     }
@@ -753,6 +695,22 @@ async function resolveWorkflowUpdateTemplate(cwd, hashes) {
         ? workflowMdTemplate
         : template.content;
 }
+function refreshNativeWorkflowProvenance(cwd) {
+    const record = loadWorkflowProvenance(cwd);
+    if (record?.source_kind !== "bundled" ||
+        record.workflow_id !== NATIVE_WORKFLOW_ID)
+        return;
+    const workflowPath = path.join(cwd, PATHS.WORKFLOW_GUIDE_FILE);
+    if (fs.existsSync(workflowPath) &&
+        fs.readFileSync(workflowPath, "utf-8") ===
+            replacePythonCommandLiterals(workflowMdTemplate)) {
+        writeWorkflowProvenance(cwd, {
+            ...record,
+            ref: VERSION,
+            content_sha256: computeHash(workflowMdTemplate),
+        });
+    }
+}
 /**
  * Analyze changes between current files and templates
  *
@@ -792,11 +750,15 @@ function analyzeChanges(cwd, hashes, templates) {
         }
         else {
             const existingContent = fs.readFileSync(fullPath, "utf-8");
-            const legacyPennixHook = migrateLegacyPennixCodexWorkflowHook(relativePath, existingContent);
-            if (legacyPennixHook?.needsUpdate &&
-                newContent === legacyPennixHook.content) {
+            const markers = relativePath === FILE_NAMES.AGENTS
+                ? [TRELLIS_BLOCK_START, TRELLIS_BLOCK_END]
+                : relativePath === COPILOT_INSTRUCTIONS_PATH
+                    ? [COPILOT_INSTRUCTIONS_BLOCK_START, COPILOT_INSTRUCTIONS_BLOCK_END]
+                    : null;
+            if (markers &&
+                mergeManagedMarkdownBlock(existingContent, newContent, markers[0], markers[1]) === null) {
                 change.status = "changed";
-                result.autoUpdateFiles.push(change);
+                result.changedFiles.push(change);
                 continue;
             }
             if (existingContent === newContent) {
@@ -1335,7 +1297,9 @@ export function classifyMigrations(migrations, cwd, hashes, templates) {
             const newExists = fs.existsSync(newPath);
             if (newExists) {
                 // Target exists - check if it only contains unmodified template files
-                if (isDirectorySafeToReplace(cwd, item.to, hashes, templates)) {
+                if (isDirectorySafeToReplace(cwd, item.to, hashes, templates) &&
+                    (!dirMatchesCurrentTemplates(cwd, item.to, templates) ||
+                        isDirectorySafeToReplace(cwd, item.from, hashes, templates))) {
                     // Safe to delete target and rename source
                     result.auto.push(item);
                 }
@@ -1562,6 +1526,11 @@ export async function executeMigrations(classified, cwd, options, templates) {
             // flavored bytes, so just drop the now-redundant source instead (#447).
             if (fs.existsSync(newPath) &&
                 dirMatchesCurrentTemplates(cwd, item.to, templates)) {
+                if (!isDirectorySafeToReplace(cwd, item.from, loadHashes(cwd), templates)) {
+                    result.skipped++;
+                    console.log(chalk.yellow("  ○ Preserved modified migration source: " + item.from));
+                    continue;
+                }
                 removeDirectoryRecursive(oldPath);
                 const hashes = loadHashes(cwd);
                 const updatedHashes = {};
@@ -1976,6 +1945,8 @@ export async function update(options) {
         }
         if (zcodeConfigured)
             printZcodeSetupHint();
+        if (!options.dryRun)
+            refreshNativeWorkflowProvenance(cwd);
         return;
     }
     // Show what this operation will do
@@ -2116,6 +2087,20 @@ export async function update(options) {
         for (const file of changes.changedFiles) {
             const action = await promptConflictResolution(file, options, applyToAll);
             if (action === "overwrite") {
+                const markers = file.relativePath === FILE_NAMES.AGENTS
+                    ? [TRELLIS_BLOCK_START, TRELLIS_BLOCK_END]
+                    : file.relativePath === COPILOT_INSTRUCTIONS_PATH
+                        ? [
+                            COPILOT_INSTRUCTIONS_BLOCK_START,
+                            COPILOT_INSTRUCTIONS_BLOCK_END,
+                        ]
+                        : null;
+                if (markers &&
+                    mergeManagedMarkdownBlock(fs.readFileSync(file.path, "utf-8"), file.newContent, markers[0], markers[1]) === null) {
+                    throw new Error("Refusing ambiguous managed Markdown markers in " +
+                        file.relativePath +
+                        "; use --create-new or repair the markers.");
+                }
                 fs.writeFileSync(file.path, file.newContent);
                 if (file.relativePath.endsWith(".sh") ||
                     file.relativePath.endsWith(".py")) {
@@ -2149,6 +2134,7 @@ export async function update(options) {
     }
     // Update version file
     updateVersionFile(cwd);
+    refreshNativeWorkflowProvenance(cwd);
     // Update template hashes for new, auto-updated, and overwritten files
     const filesToHash = new Map(unchangedFileHashRepairs);
     for (const file of changes.newFiles) {