chore: rebrand aios → aiox across entire codebase (#552)

* chore: rename .aios-core to .aiox-core (directory structure)

Rename all files from .aios-core/ to .aiox-core/ as part of the
AIOS → AIOX rebranding effort. This commit contains only the
directory/file renames without content modifications.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* chore: update aios→aiox references in file contents

Replace all internal references from 'aios' to 'aiox' across the
codebase — imports, paths, config files, docs, tests, and scripts.
Completes the AIOS → AIOX rebranding at the content level.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(hooks): add wrappers to prevent stdout→stderr leak in Claude Code

process.exit() in hook scripts causes unflushed stdout buffers to
spill into stderr when Claude Code runs hooks via pipes. This triggers
false "UserPromptSubmit hook error" on every prompt.

Added synapse-wrapper.cjs and precompact-wrapper.cjs that run the
real hooks as child processes via execFileSync, isolating stdout/stderr
in memory buffers. Also updated settings.json to use the wrappers and
applied aios→aiox references in hook files.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* chore: update entity-registry, gitignore hooks, remove stale doc

- Update entity-registry.yaml with aiox references
- Simplify .gitignore hooks exclusion pattern
- Remove obsolete bob-orchestrator-workflow doc

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(test): update gitignore assertion to match simplified hooks exclusion

The .gitignore now uses !.claude/hooks/ (all hooks) instead of
individual file exceptions. Updated test to match.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix(security): resolve CodeQL alerts — incomplete sanitization, URL check, shell injection

- framework-guard: escape regex-special chars properly before glob conversion
- squad-downloader.test: use URL hostname comparison instead of substring includes
- package-synapse: use execFileSync instead of execSync to prevent shell injection

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: oalanicolas

.aios-core/infrastructure/templates/gitignore/gitignore-brownfield-merge.tmpl

@@ -4,11 +4,11 @@
  * CLI commands for the layered configuration system (ADR-PRO-002).
  *
  * Subcommands:
- *   aios config show [--level <n>] [--app <name>] [--debug]
- *   aios config diff --levels <a>,<b>
- *   aios config migrate [--dry-run] [--force]
- *   aios config validate [--level <n>]
- *   aios config init-local
+ *   aiox config show [--level <n>] [--app <name>] [--debug]
+ *   aiox config diff --levels <a>,<b>
+ *   aiox config migrate [--dry-run] [--force]
+ *   aiox config validate [--level <n>]
+ *   aiox config init-local
  *
  * @module cli/commands/config
  * @version 1.0.0
@@ -22,7 +22,7 @@ const path = require('path');
 const fs = require('fs');
 const yaml = require('js-yaml');
 
-// Resolve core config modules (relative from .aios-core/cli/commands/config/)
+// Resolve core config modules (relative from .aiox-core/cli/commands/config/)
 const configResolverPath = path.resolve(__dirname, '..', '..', '..', 'core', 'config', 'config-resolver');
 const mergeUtilsPath = path.resolve(__dirname, '..', '..', '..', 'core', 'config', 'merge-utils');
 const envInterpolatorPath = path.resolve(__dirname, '..', '..', '..', 'core', 'config', 'env-interpolator');
@@ -45,7 +45,7 @@ function getProjectRoot() {
 }
 
 // ---------------------------------------------------------------------------
-// aios config show
+// aiox config show
 // ---------------------------------------------------------------------------
 
 function showAction(options) {
@@ -113,7 +113,7 @@ function printDebugConfig(config, sources, prefix = '') {
 }
 
 // ---------------------------------------------------------------------------
-// aios config diff
+// aiox config diff
 // ---------------------------------------------------------------------------
 
 function diffAction(options) {
@@ -198,7 +198,7 @@ function formatValue(v) {
 }
 
 // ---------------------------------------------------------------------------
-// aios config migrate
+// aiox config migrate
 // ---------------------------------------------------------------------------
 
 function migrateAction(options) {
@@ -253,20 +253,20 @@ function migrateAction(options) {
     console.log(`Backup created: ${backupPath}`);
 
     // Write split files
-    const header1 = '# AIOS Framework Configuration (Level 1)\n# DO NOT EDIT — Part of the AIOS framework.\n# Override in project-config.yaml or local-config.yaml.\n\n';
+    const header1 = '# AIOX Framework Configuration (Level 1)\n# DO NOT EDIT — Part of the AIOX framework.\n# Override in project-config.yaml or local-config.yaml.\n\n';
     fs.writeFileSync(fwPath, header1 + yaml.dump(l1Sections, { lineWidth: 120 }));
     console.log(`Created: ${CONFIG_FILES.framework}`);
 
-    const header2 = '# AIOS Project Configuration (Level 2)\n# Project-specific settings shared across the team.\n\n';
+    const header2 = '# AIOX Project Configuration (Level 2)\n# Project-specific settings shared across the team.\n\n';
     fs.writeFileSync(projPath, header2 + yaml.dump(l2Sections, { lineWidth: 120 }));
     console.log(`Created: ${CONFIG_FILES.project}`);
 
-    const header4 = '# AIOS Local Configuration (Level 4)\n# Machine-specific overrides. DO NOT commit to git.\n\n';
+    const header4 = '# AIOX Local Configuration (Level 4)\n# Machine-specific overrides. DO NOT commit to git.\n\n';
     fs.writeFileSync(localPath, header4 + yaml.dump(l4Sections, { lineWidth: 120 }));
     console.log(`Created: ${CONFIG_FILES.local}`);
 
     // Update .gitignore if needed
-    ensureGitignore(root, '.aios-core/local-config.yaml');
+    ensureGitignore(root, '.aiox-core/local-config.yaml');
 
     // Validate: resolved config should match original
     const resolved = resolveConfig(root, { skipCache: true });
@@ -277,7 +277,7 @@ function migrateAction(options) {
       console.log('\nValidation: PASS — Resolved config matches original.');
     } else {
       console.log('\nValidation: WARNING — Resolved config differs from original.');
-      console.log('This may be expected due to key normalization. Run `aios config diff` to inspect.');
+      console.log('This may be expected due to key normalization. Run `aiox config diff` to inspect.');
     }
 
     console.log('\nMigration complete. Original preserved at core-config.yaml.backup');
@@ -295,7 +295,7 @@ function splitL1(config) {
 
   // metadata (framework portion)
   if (config.markdownExploder !== undefined) l1.markdownExploder = config.markdownExploder;
-  l1.metadata = { name: 'Synkra AIOS', framework_version: '3.12.0' };
+  l1.metadata = { name: 'Synkra AIOX', framework_version: '3.12.0' };
 
   // resource_locations (Section 3)
   if (config.toolsLocation) l1.resource_locations = { tools_dir: config.toolsLocation };
@@ -443,7 +443,7 @@ function ensureGitignore(root, entry) {
 }
 
 // ---------------------------------------------------------------------------
-// aios config validate
+// aiox config validate
 // ---------------------------------------------------------------------------
 
 function validateAction(options) {
@@ -523,16 +523,16 @@ function validateYamlSyntax(root, level, issues) {
 }
 
 // ---------------------------------------------------------------------------
-// aios config init-local
+// aiox config init-local
 // ---------------------------------------------------------------------------
 
 function initLocalAction() {
   const root = getProjectRoot();
-  const templatePath = path.join(root, '.aios-core', 'local-config.yaml.template');
-  const targetPath = path.join(root, '.aios-core', 'local-config.yaml');
+  const templatePath = path.join(root, '.aiox-core', 'local-config.yaml.template');
+  const targetPath = path.join(root, '.aiox-core', 'local-config.yaml');
 
   if (!fs.existsSync(templatePath)) {
-    console.error('Template not found: .aios-core/local-config.yaml.template');
+    console.error('Template not found: .aiox-core/local-config.yaml.template');
     process.exit(1);
   }
 
@@ -542,26 +542,26 @@ function initLocalAction() {
   }
 
   fs.copyFileSync(templatePath, targetPath);
-  console.log('Created: .aios-core/local-config.yaml (from template)');
+  console.log('Created: .aiox-core/local-config.yaml (from template)');
   console.log('Edit this file to customize your machine-specific settings.');
 
   // Ensure gitignore
-  ensureGitignore(root, '.aios-core/local-config.yaml');
+  ensureGitignore(root, '.aiox-core/local-config.yaml');
 }
 
 // ---------------------------------------------------------------------------
 // Command builder
 // ---------------------------------------------------------------------------
 
 /**
- * Create the `aios config` command with all subcommands.
+ * Create the `aiox config` command with all subcommands.
  * @returns {Command}
  */
 function createConfigCommand() {
   const configCmd = new Command('config')
     .description('Manage layered configuration (ADR-PRO-002)');
 
-  // aios config show
+  // aiox config show
   configCmd
     .command('show')
     .description('Show resolved configuration')
@@ -570,30 +570,30 @@ function createConfigCommand() {
     .option('-d, --debug', 'Show source annotations for each value')
     .action(showAction);
 
-  // aios config diff
+  // aiox config diff
   configCmd
     .command('diff')
     .description('Compare configuration between two levels')
     .requiredOption('--levels <a,b>', 'Two levels to compare (e.g., 1,2)')
     .option('-a, --app <name>', 'Include app-specific context')
     .action(diffAction);
 
-  // aios config migrate
+  // aiox config migrate
   configCmd
     .command('migrate')
     .description('Migrate monolithic core-config.yaml to layered files')
     .option('--dry-run', 'Preview without writing files')
     .option('--force', 'Overwrite existing split files')
     .action(migrateAction);
 
-  // aios config validate
+  // aiox config validate
   configCmd
     .command('validate')
     .description('Validate YAML syntax and lint config files')
     .option('-l, --level <level>', 'Validate specific level only')
     .action(validateAction);
 
-  // aios config init-local
+  // aiox config init-local
   configCmd
     .command('init-local')
     .description('Create local-config.yaml from template')

.aios-core/monitor/hooks/lib/__init__.py

@@ -21,17 +21,17 @@ function createManifestCommand() {
   const manifest = new Command('manifest');
 
   manifest
-    .description('Manage AIOS manifest files for agents, workers, and tasks')
+    .description('Manage AIOX manifest files for agents, workers, and tasks')
     .addHelpText('after', `
 Commands:
   validate          Validate all manifest files
   regenerate        Regenerate manifests from source files
 
 Examples:
-  $ aios manifest validate
-  $ aios manifest validate --verbose
-  $ aios manifest regenerate
-  $ aios manifest regenerate --force
+  $ aiox manifest validate
+  $ aiox manifest validate --verbose
+  $ aiox manifest regenerate
+  $ aiox manifest regenerate --force
 `);
 
   // Add subcommands

.aios-core/product/templates/ide-rules/codex-rules.md

@@ -31,7 +31,7 @@ function createRegenerateCommand() {
         });
 
         if (!options.dryRun) {
-          console.log('Scanning .aios-core/...\n');
+          console.log('Scanning .aiox-core/...\n');
         } else {
           console.log('[DRY RUN] Would generate:\n');
         }

.aios-core/cli/commands/config/index.js .aiox-core/cli/commands/config/index.js.aios-core/cli/commands/config/index.js renamed to .aiox-core/cli/commands/config/index.js

@@ -72,31 +72,31 @@ async function executeAdd(server, options) {
       console.log('');
     }
 
-    console.log('Usage: aios mcp add <server-name>');
-    console.log('Example: aios mcp add context7');
+    console.log('Usage: aiox mcp add <server-name>');
+    console.log('Example: aiox mcp add context7');
     return;
   }
 
   // Check global config exists
   if (!globalConfigExists()) {
     console.error('❌ Global MCP config not found.');
-    console.log('Run "aios mcp setup" first to create global configuration.');
+    console.log('Run "aiox mcp setup" first to create global configuration.');
     process.exit(1);
   }
 
   // Server name required for most operations
   if (!server) {
     console.error('❌ Server name required.');
-    console.log('Usage: aios mcp add <server-name>');
+    console.log('Usage: aiox mcp add <server-name>');
     console.log('');
     console.log('Available templates:');
     for (const name of getAvailableTemplates()) {
       console.log(`  - ${name}`);
     }
     console.log('');
     console.log('Or provide custom config:');
-    console.log('  aios mcp add myserver --type sse --url https://example.com/mcp');
-    console.log('  aios mcp add myserver --command npx --args "-y,@scope/mcp-server"');
+    console.log('  aiox mcp add myserver --type sse --url https://example.com/mcp');
+    console.log('  aiox mcp add myserver --command npx --args "-y,@scope/mcp-server"');
     process.exit(1);
   }
 
@@ -220,8 +220,8 @@ async function executeAdd(server, options) {
         console.log(`  - ${name}`);
       }
       console.log('\nOr provide custom config:');
-      console.log(`  aios mcp add ${server} --type sse --url <url>`);
-      console.log(`  aios mcp add ${server} --command npx --args "-y,@scope/server"`);
+      console.log(`  aiox mcp add ${server} --type sse --url <url>`);
+      console.log(`  aiox mcp add ${server} --command npx --args "-y,@scope/server"`);
     }
 
     process.exit(1);