fix: fence native project inputs before legacy operations

docs/reference/native-config-compiler.md

@@ -1,11 +1,30 @@
 # Native config compiler foundation
 
 This is an experimental, pure compiler for a bounded subset of the planned
-`.hack/hack.project.json` format. It does not discover projects, execute workloads,
+`.hack/hack.project.json` format. The compiler does not discover projects, execute workloads,
 import Compose, migrate data, decrypt environment values, perform host admission,
 or change how existing projects run. A successful compile is syntax and semantic
 validation, not backend capability or application acceptance.
 
+The CLI recognizes this filename as a project boundary. Native runtime and adoption
+are not enabled yet: legacy project commands refuse with
+`E_NATIVE_PROJECT_UNSUPPORTED`. If active `.hack/` or `.dev/` Compose, JSON or TOML
+inputs also exist, they refuse with `E_NATIVE_PROJECT_CONFLICT`. The marker still
+blocks fallback when malformed, a future version, a directory or a dangling link.
+Filesystem inspection failures also refuse. Generated internal files, branch files,
+backups and a root-level Compose file are not competing authored Hack inputs.
+
+Discovery never crosses a native boundary to select an ancestor Compose project.
+Registered name/ID lookup checks the stored root directly. Project listing marks
+blocked registered entries `unavailable`, includes `input_diagnostic`, and continues
+listing other entries without parsing the blocked legacy configuration. Global
+configuration and explicit offline validation remain available. Init, legacy env
+repair, config writes and domain migration/rollback refuse before modifying native
+input; a refused rollback preserves its recovery journal. Selection is checked
+again at mutation boundaries, but this is not atomic protection against concurrent
+external edits. Locked adoption belongs to a later integration step.
+`hack env get` retains its fixed redacted failure message and empty stdout.
+
 The standalone `packages/config-compiler` Rust package has no dependency on the
 native runtime, virtualization, Docker, or platform provider APIs. It uses the
 repository's pinned Rust 1.97.1 and committed Cargo lockfile when building. The

src/commands/config.ts

@@ -22,6 +22,7 @@ import { ensureDir, readTextFile, writeTextFileIfChanged } from "../lib/fs.ts";
 import { isRecord } from "../lib/guards.ts";
 import type { ProjectContext } from "../lib/project.ts";
 import { findProjectContext } from "../lib/project.ts";
+import { assertLegacyProjectDirectory } from "../lib/project-input-selection.ts";
 import { normalizeProjectName } from "../lib/project-name.ts";
 import {
   resolveRegisteredProjectByName,
@@ -187,6 +188,10 @@ const handleConfigSet: CommandHandlerFor<typeof configSetSpec> = async ({
   const nextText = `${JSON.stringify(read.value, null, 2)}\n`;
   if (project.scope === "global") {
     await ensureDir(dirname(read.path));
+  } else {
+    await assertLegacyProjectDirectory({
+      projectDir: project.project.projectDir,
+    });
   }
   const result = await writeTextFileIfChanged(read.path, nextText);
 
@@ -329,6 +334,9 @@ async function readConfigObject(opts: {
     opts.target.project.projectDir,
     PROJECT_CONFIG_FILENAME
   );
+  await assertLegacyProjectDirectory({
+    projectDir: opts.target.project.projectDir,
+  });
   const jsonText = await readTextFile(jsonPath);
   if (jsonText !== null) {
     const parsed = parseJsonObject({ text: jsonText, path: jsonPath });
@@ -381,6 +389,9 @@ async function readConfigJsonForSet(opts: {
     opts.target.project.projectDir,
     PROJECT_CONFIG_FILENAME
   );
+  await assertLegacyProjectDirectory({
+    projectDir: opts.target.project.projectDir,
+  });
   const jsonText = await readTextFile(jsonPath);
   if (jsonText === null) {
     const tomlPath = resolve(

src/commands/doctor.ts

@@ -121,6 +121,7 @@ import {
   repairLegacyComposeEnvFileReferences,
   resolveProjectEnvConfig,
 } from "../lib/project-env-config.ts";
+import { assertLegacyProjectDiscovery } from "../lib/project-input-selection.ts";
 import {
   inspectProjectLifecycleHygiene,
   repairProjectLifecycleSessions,
@@ -443,6 +444,9 @@ async function maybeRunNativeMappingRecovery(
 const handleDoctor: CommandHandlerFor<typeof doctorSpec> = async ({
   args,
 }): Promise<number> => {
+  await assertLegacyProjectDiscovery({
+    startDir: resolveDoctorStartDir(args.options.path),
+  });
   const mappingResult = await maybeRunNativeMappingRecovery(args);
   if (mappingResult !== null) {
     return mappingResult;
@@ -889,6 +893,10 @@ const handleDoctor: CommandHandlerFor<typeof doctorSpec> = async ({
   return 0;
 };
 
+function resolveDoctorStartDir(pathOption: string | undefined): string {
+  return resolve(process.cwd(), pathOption ?? ".");
+}
+
 async function handleNativeDoctor(opts: {
   readonly runtime: NativeRuntimeSelection;
   readonly browser: ReturnType<typeof parseBrowserNetworkOptions>;
@@ -3181,6 +3189,7 @@ async function maybeMigrateProjectEnvConfig(opts: {
 
   const removed = await removeLegacyProjectEnvArtifacts({
     paths: cleanupCandidates,
+    projectRoot: project.projectRoot,
   });
   if (removed.length > 0) {
     note(`Removed ${removed.join(", ")}`, "env cleanup");