feat(cli): migrate all setup steps to use local state for completion tracking

Update every setup step to write completed_steps to .ktx/setup/state.json
instead of ktx.yaml, stripping legacy entries from config on write.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

packages/cli/src/setup-models.ts

@@ -6,8 +6,9 @@ import {
   type KtxProjectConfig,
   type KtxProjectLlmConfig,
   loadKtxProject,
-  markKtxSetupStepComplete,
+  markKtxSetupStateStepComplete,
   serializeKtxProjectConfig,
+  stripKtxSetupCompletedSteps,
 } from '@ktx/context/project';
 import { type KtxLlmConfig, type KtxLlmHealthCheckResult, runKtxLlmHealthCheck } from '@ktx/llm';
 import type { KtxCliIo } from './cli-runtime.js';
@@ -361,7 +362,7 @@ async function chooseModel(
 
 async function persistLlmConfig(projectDir: string, credentialRef: string, model: string): Promise<void> {
   const project = await loadKtxProject({ projectDir });
-  const config = markKtxSetupStepComplete(
+  const config = stripKtxSetupCompletedSteps(
     {
       ...project.config,
       llm: buildProjectLlmConfig(project.config.llm, credentialRef, model),
@@ -373,9 +374,9 @@ async function persistLlmConfig(projectDir: string, credentialRef: string, model
         },
       },
     },
-    'llm',
   );
   await writeFile(project.configPath, serializeKtxProjectConfig(config), 'utf-8');
+  await markKtxSetupStateStepComplete(projectDir, 'llm');
 }
 
 function buildInteractiveRetryArgs(args: KtxSetupModelArgs): KtxSetupModelArgs {