@danielblomma/cortex-mcp 2.0.18 → 2.0.19

package/README.md

@@ -97,7 +97,7 @@ cortex init --bootstrap
 
 This will:
 
-- scaffold `.context/`, `scripts/`, `mcp/`, `.githooks/`, and docs files
+- scaffold `.context/`, `.context/scripts/`, `.context/mcp/`, `.githooks/`, and docs files
 - activate git hooks for checkout, pull/merge, commit, and rewrite events
 - build and prepare the local MCP server
 - try to auto-register MCP connections for Claude/Codex (if installed)

package/bin/cortex.mjs

@@ -27,11 +27,14 @@ const PACKAGE_JSON_PATH = path.join(PACKAGE_ROOT, "package.json");
 // only the three editable config files". Generated artifacts (db,
 // embeddings, cache, hooks, mcp/, govern.local.json) never land in git.
 const MCP_PROJECT_REL = path.join(".context", "mcp");
+const CONTEXT_SCRIPTS_REL = path.join(".context", "scripts");
 
+// `.context/*` (not `.context/`) so the !-negations below actually re-include
+// the config files — git can't re-include children of an excluded directory.
 const GITIGNORE_LINES = [
   "",
   "# Cortex local storage",
-  ".context/",
+  ".context/*",
   "!.context/config.yaml",
   "!.context/rules.yaml",
   "!.context/ontology.cypher",
@@ -461,12 +464,73 @@ function migrateLegacyMcpLocation(targetDir) {
   );
 }
 
+const LEGACY_SCRIPT_ENTRIES = [
+  "bootstrap.sh",
+  "context.sh",
+  "dashboard.mjs",
+  "dashboard.sh",
+  "doctor.sh",
+  "embed.sh",
+  "ingest.mjs",
+  "ingest.sh",
+  "install-git-hooks.sh",
+  "load-kuzu.sh",
+  "load-ryu.sh",
+  "memory-compile.mjs",
+  "memory-compile.sh",
+  "memory-lint.mjs",
+  "memory-lint.sh",
+  "refresh.sh",
+  "status.sh",
+  "update-context.sh",
+  "watch.sh",
+  "lib",
+  "parsers"
+];
+
+function looksLikeLegacyCortexScriptsDir(scriptsDir) {
+  const contextScript = path.join(scriptsDir, "context.sh");
+  if (!fs.existsSync(contextScript)) {
+    return false;
+  }
+  try {
+    const contents = fs.readFileSync(contextScript, "utf8");
+    return contents.includes("bootstrap)") && contents.includes("graph-load)") && contents.includes("memory-lint)");
+  } catch {
+    return false;
+  }
+}
+
+function removeLegacyCortexScripts(targetDir) {
+  if (path.resolve(targetDir) === PACKAGE_ROOT) {
+    return;
+  }
+
+  const scriptsDir = path.join(targetDir, "scripts");
+  if (!looksLikeLegacyCortexScriptsDir(scriptsDir)) {
+    return;
+  }
+
+  for (const entry of LEGACY_SCRIPT_ENTRIES) {
+    fs.rmSync(path.join(scriptsDir, entry), { recursive: true, force: true });
+  }
+
+  try {
+    if (fs.existsSync(scriptsDir) && fs.readdirSync(scriptsDir).length === 0) {
+      fs.rmdirSync(scriptsDir);
+    }
+  } catch {
+    // Best effort. A user's own files in scripts/ must remain untouched.
+  }
+}
+
 function installScaffold(targetDir, force) {
   migrateLegacyMcpLocation(targetDir);
+  removeLegacyCortexScripts(targetDir);
 
   const copyMap = [
     [path.join(SCAFFOLD_ROOT, ".context"), path.join(targetDir, ".context")],
-    [path.join(SCAFFOLD_ROOT, "scripts"), path.join(targetDir, "scripts")],
+    [path.join(SCAFFOLD_ROOT, "scripts"), path.join(targetDir, CONTEXT_SCRIPTS_REL)],
     [path.join(SCAFFOLD_ROOT, "mcp"), path.join(targetDir, MCP_PROJECT_REL)],
     [path.join(SCAFFOLD_ROOT, ".githooks"), path.join(targetDir, ".githooks")]
   ];
@@ -720,7 +784,7 @@ async function connectMcpClients(targetDir, options = {}) {
 }
 
 async function maybeInstallGitHooks(targetDir) {
-  const installScript = path.join(targetDir, "scripts", "install-git-hooks.sh");
+  const installScript = path.join(targetDir, CONTEXT_SCRIPTS_REL, "install-git-hooks.sh");
   if (!fs.existsSync(installScript)) {
     return false;
   }
@@ -758,16 +822,17 @@ function isTruthyEnv(value) {
 function canAutoInitialize(targetDir) {
   // Legacy mcp/ at root no longer counted — pre-v2.0.5 projects are migrated
   // by installScaffold rather than blocking auto-init.
-  const scaffoldPaths = [".context", "scripts", ".githooks"].map((entry) => path.join(targetDir, entry));
+  const scaffoldPaths = [".context", ".githooks"].map((entry) => path.join(targetDir, entry));
   return scaffoldPaths.every((entryPath) => !fs.existsSync(entryPath));
 }
 
 function isScaffoldOutOfDate(targetDir) {
-  const contextScript = path.join(targetDir, "scripts", "context.sh");
+  const contextScript = path.join(targetDir, CONTEXT_SCRIPTS_REL, "context.sh");
+  const legacyContextScript = path.join(targetDir, "scripts", "context.sh");
   if (!fs.existsSync(contextScript)) {
-    return false;
+    return fs.existsSync(legacyContextScript);
   }
-  const doctorScript = path.join(targetDir, "scripts", "doctor.sh");
+  const doctorScript = path.join(targetDir, CONTEXT_SCRIPTS_REL, "doctor.sh");
   if (!fs.existsSync(doctorScript)) {
     return true;
   }
@@ -812,7 +877,7 @@ async function maybeMigrateScaffold(targetDir, command) {
 
   console.error(
     `[cortex] scaffold in ${targetDir} is out of date ` +
-      `(missing scripts/doctor.sh, .context/mcp/package.json, doctor subcommand in context.sh, ` +
+      `(missing .context/scripts/doctor.sh, .context/mcp/package.json, doctor subcommand in context.sh, ` +
       `or carries a legacy mcp/ directory at the project root).`
   );
 
@@ -881,7 +946,7 @@ async function ensureProjectInitializedForMcp(targetDir) {
 }
 
 async function runContextCommand(cwd, contextArgs) {
-  const contextScript = path.join(cwd, "scripts", "context.sh");
+  const contextScript = path.join(cwd, CONTEXT_SCRIPTS_REL, "context.sh");
   if (!fs.existsSync(contextScript)) {
     throw new Error(`Missing ${contextScript}. Run 'cortex init' first.`);
   }
@@ -915,7 +980,7 @@ async function run() {
     await maybeInstallGitHooks(target);
 
     console.log(`[cortex] initialized in ${target}`);
-    console.log("[cortex] scaffold copied: .context/, scripts/, mcp/, .githooks/, docs/");
+    console.log("[cortex] scaffold copied: .context/, .context/scripts/, .context/mcp/, .githooks/, docs/");
     console.log(`[cortex] Claude commands ready: /context-update (${helpers.claude.total} files)`);
     if (helpers.codex.changed) {
       console.log("[cortex] Codex workflow instructions added to AGENTS.md");

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@danielblomma/cortex-mcp",
   "mcpName": "io.github.DanielBlomma/cortex",
-  "version": "2.0.18",
+  "version": "2.0.19",
   "description": "Local, repo-scoped context platform for coding assistants. Semantic search, graph relationships, and architectural rule context.",
   "type": "module",
   "author": "Daniel Blomma",
@@ -49,6 +49,7 @@
     "docs/MCP_MARKETPLACE.md"
   ],
   "scripts": {
+    "pretest": "test -d scaffold/scripts/parsers/node_modules || npm --prefix scaffold/scripts/parsers install --no-fund --no-update-notifier --silent",
     "test": "node tests/context-regressions.test.mjs && node --test tests/ingest-units.test.mjs tests/javascript-parser.test.mjs tests/sql-parser.test.mjs tests/config-parser.test.mjs tests/resources-parser.test.mjs tests/vbnet-parser.test.mjs tests/cpp-parser.test.mjs tests/dashboard.test.mjs tests/init-config.test.mjs tests/init-agents.test.mjs tests/multi-level.test.mjs tests/no-legacy-paths.test.mjs tests/tree-sitter-error-reporting.test.mjs tests/tree-sitter-body-cap.test.mjs tests/tree-sitter-exported.test.mjs tests/tree-sitter-robustness.test.mjs",
     "release:sync-version": "node scripts/sync-release-version.mjs",
     "release:check-version-sync": "node scripts/sync-release-version.mjs --check",

package/scaffold/.context/config.yaml

@@ -1,11 +1,10 @@
 repo_id: cortex
 source_paths:
-  - src
+  - scripts
+  - mcp/src
   - docs
-  - design
   - .context/notes
   - .context/decisions
-  - README.md
 truth_order:
   - ADR
   - RULE

package/scaffold/.githooks/_cortex-update-runner.sh

@@ -6,12 +6,12 @@ if [[ -z "$REPO_ROOT" ]]; then
   exit 0
 fi
 
-CONTEXT_SCRIPT="$REPO_ROOT/scripts/context.sh"
+CONTEXT_SCRIPT="$REPO_ROOT/.context/scripts/context.sh"
 if [[ ! -x "$CONTEXT_SCRIPT" ]]; then
   exit 0
 fi
 
-PARSER_MODULES_DIR="$REPO_ROOT/scripts/parsers/node_modules"
+PARSER_MODULES_DIR="$REPO_ROOT/.context/scripts/parsers/node_modules"
 
 HOOK_DIR="$REPO_ROOT/.context/hooks"
 LOCK_DIR="$HOOK_DIR/update.lock"

package/scaffold/mcp/src/embeddings.ts

@@ -101,7 +101,7 @@ export function loadEmbeddingIndex(): EmbeddingIndex {
     embeddingsCache = {
       model: null,
       vectors: new Map(),
-      warning: "Embedding index missing (run: ./scripts/context.sh embed)"
+      warning: "Embedding index missing (run: cortex embed)"
     };
     return embeddingsCache;
   }

package/scaffold/mcp/src/graph.ts

@@ -419,8 +419,8 @@ function readGraphSignature(): string | null {
 
 function buildMissingDbMessage(): string {
   const dbDir = path.dirname(DB_PATH);
-  const loadCommand = "./scripts/context.sh graph-load";
-  const bootstrapCommand = "./scripts/context.sh bootstrap";
+  const loadCommand = "cortex graph-load";
+  const bootstrapCommand = "cortex bootstrap";
 
   if (!fs.existsSync(dbDir)) {
     return `RyuGraph directory missing at ${dbDir}. Run ${bootstrapCommand}.`;
@@ -430,7 +430,7 @@ function buildMissingDbMessage(): string {
 }
 
 function buildIncompatibleGraphMessage(missingKeys: string[]): string {
-  const loadCommand = "./scripts/context.sh graph-load";
+  const loadCommand = "cortex graph-load";
   const missing = missingKeys.join(", ");
   return `RyuGraph manifest is missing schema keys (${missing}). Run ${loadCommand} to rebuild the graph DB.`;
 }

package/scaffold/scripts/bootstrap.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MCP_DIR="$REPO_ROOT/.context/mcp"
 TOTAL_STEPS=6
 STEP_INDEX=0
@@ -25,24 +26,24 @@ mkdir -p "$MCP_DIR/.npm-cache"
 step "Installing MCP dependencies"
 info "note: upstream RyuGraph dependencies may print deprecation warnings during install"
 NPM_CONFIG_CACHE="$MCP_DIR/.npm-cache" npm --prefix "$MCP_DIR" install --no-fund --no-update-notifier --loglevel=warn
-NPM_CONFIG_CACHE="$REPO_ROOT/scripts/parsers/.npm-cache" npm --prefix "$REPO_ROOT/scripts/parsers" install --no-fund --no-update-notifier --loglevel=warn
+NPM_CONFIG_CACHE="$REPO_ROOT/.context/scripts/parsers/.npm-cache" npm --prefix "$REPO_ROOT/.context/scripts/parsers" install --no-fund --no-update-notifier --loglevel=warn
 
-source "$REPO_ROOT/scripts/lib/enterprise-check.sh"
+source "$SCRIPT_DIR/lib/enterprise-check.sh"
 
 step "Indexing repository context"
-"$REPO_ROOT/scripts/ingest.sh"
+"$SCRIPT_DIR/ingest.sh"
 
 step "Generating semantic embeddings"
-if ! "$REPO_ROOT/scripts/embed.sh"; then
+if ! "$SCRIPT_DIR/embed.sh"; then
   info "warning: embedding generation failed; continuing with lexical search fallback"
 fi
 
 step "Loading RyuGraph"
-"$REPO_ROOT/scripts/load-ryu.sh"
+"$SCRIPT_DIR/load-ryu.sh"
 
 step "Reading context status"
-"$REPO_ROOT/scripts/status.sh"
+"$SCRIPT_DIR/status.sh"
 
 echo ""
 info "bootstrap complete"
-info "next: run ./scripts/context.sh update while coding"
+info "next: run cortex update while coding"

package/scaffold/scripts/context.sh

@@ -5,7 +5,7 @@ SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 print_help() {
   cat <<'EOF'
-Usage: ./scripts/context.sh <command> [options]
+Usage: cortex <command> [options]
 
 Commands:
   bootstrap                        Install deps + full ingest + graph load

package/scaffold/scripts/dashboard.mjs

@@ -6,7 +6,9 @@ import { execSync } from "node:child_process";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const REPO_ROOT = path.resolve(__dirname, "..");
+const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
+  ? path.resolve(process.env.CORTEX_PROJECT_ROOT)
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const CACHE_DIR = path.join(CONTEXT_DIR, "cache");
 const CONFIG_PATH = path.join(CONTEXT_DIR, "config.yaml");

package/scaffold/scripts/dashboard.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -euo pipefail
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-REPO_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MANIFEST="$REPO_ROOT/.context/cache/manifest.json"
 
 if [[ ! -f "$MANIFEST" ]]; then

package/scaffold/scripts/doctor.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 MCP_DIR="$CONTEXT_DIR/mcp"
 

package/scaffold/scripts/embed.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MCP_DIR="$REPO_ROOT/.context/mcp"
 
 if ! command -v npm >/dev/null 2>&1; then

package/scaffold/scripts/ingest.mjs

@@ -91,7 +91,9 @@ async function loadOptionalParsers() {
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const REPO_ROOT = path.resolve(__dirname, "..");
+const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
+  ? path.resolve(process.env.CORTEX_PROJECT_ROOT)
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const CACHE_DIR = path.join(CONTEXT_DIR, "cache");
 const DB_IMPORT_DIR = path.join(CONTEXT_DIR, "db", "import");

package/scaffold/scripts/ingest.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 
 printf "[ingest] repo: %s\n" "$REPO_ROOT"
@@ -17,4 +18,4 @@ if ! command -v node >/dev/null 2>&1; then
   exit 1
 fi
 
-node "$REPO_ROOT/scripts/ingest.mjs" "$@"
+node "$SCRIPT_DIR/ingest.mjs" "$@"

package/scaffold/scripts/install-git-hooks.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 HOOKS_DIR="$REPO_ROOT/.githooks"
 
 if [[ ! -d "$HOOKS_DIR" ]]; then

package/scaffold/scripts/load-kuzu.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 echo "[graph-load] warning: load-kuzu.sh is deprecated; using RyuGraph loader"
-"$REPO_ROOT/scripts/load-ryu.sh" "$@"
+"$SCRIPT_DIR/load-ryu.sh" "$@"

package/scaffold/scripts/load-ryu.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MCP_DIR="$REPO_ROOT/.context/mcp"
 
 if [[ ! -f "$MCP_DIR/package.json" ]]; then

package/scaffold/scripts/memory-compile.mjs

@@ -2,7 +2,7 @@
 import fs from "node:fs";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
-import { parseFrontmatter, parseStringList } from "../.context/mcp/dist/frontmatter.js";
+import { parseFrontmatter, parseStringList } from "../mcp/dist/frontmatter.js";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -17,7 +17,7 @@ function normalizeForWsl(rawPath) {
 
 const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
   ? path.resolve(normalizeForWsl(process.env.CORTEX_PROJECT_ROOT))
-  : path.resolve(__dirname, "..");
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const MEMORY_DIR = path.join(CONTEXT_DIR, "memory");
 const RAW_DIR = path.join(MEMORY_DIR, "raw");

package/scaffold/scripts/memory-compile.sh

@@ -2,7 +2,8 @@
 # Keep in sync with scripts/memory-compile.sh
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 
 printf "[memory-compile] repo: %s\n" "$REPO_ROOT"
@@ -17,4 +18,4 @@ if ! command -v node >/dev/null 2>&1; then
   exit 1
 fi
 
-node "$REPO_ROOT/scripts/memory-compile.mjs" "$@"
+CORTEX_PROJECT_ROOT="$REPO_ROOT" node "$SCRIPT_DIR/memory-compile.mjs" "$@"

package/scaffold/scripts/memory-lint.mjs

@@ -2,7 +2,7 @@
 import fs from "node:fs";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
-import { parseFrontmatter, parseStringList } from "../.context/mcp/dist/frontmatter.js";
+import { parseFrontmatter, parseStringList } from "../mcp/dist/frontmatter.js";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -17,7 +17,7 @@ function normalizeForWsl(rawPath) {
 
 const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
   ? path.resolve(normalizeForWsl(process.env.CORTEX_PROJECT_ROOT))
-  : path.resolve(__dirname, "..");
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const MEMORY_DIR = path.join(CONTEXT_DIR, "memory");
 const COMPILED_DIR = path.join(MEMORY_DIR, "compiled");

package/scaffold/scripts/memory-lint.sh

@@ -2,7 +2,8 @@
 # Keep in sync with scripts/memory-lint.sh
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 
 printf "[memory-lint] repo: %s\n" "$REPO_ROOT"
@@ -17,4 +18,4 @@ if ! command -v node >/dev/null 2>&1; then
   exit 1
 fi
 
-node "$REPO_ROOT/scripts/memory-lint.mjs" "$@"
+CORTEX_PROJECT_ROOT="$REPO_ROOT" node "$SCRIPT_DIR/memory-lint.mjs" "$@"

package/scaffold/scripts/parsers/package-lock.json

@@ -21,7 +21,6 @@
       "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.16.0.tgz",
       "integrity": "sha512-UVJyE9MttOsBQIDKw1skb9nAwQuR5wuGD3+82K6JgJlm/Y+KI92oNsMNGZCYdDsVtRHSak0pcV5Dno5+4jh9sw==",
       "license": "MIT",
-      "peer": true,
       "bin": {
         "acorn": "bin/acorn"
       },

package/scaffold/scripts/refresh.sh

@@ -1,9 +1,9 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 echo "[refresh] running ingestion"
-"$REPO_ROOT/scripts/ingest.sh" "$@"
+"$SCRIPT_DIR/ingest.sh" "$@"
 
 echo "[refresh] done"

package/scaffold/scripts/status.sh

@@ -1,14 +1,15 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MANIFEST="$REPO_ROOT/.context/cache/manifest.json"
 GRAPH_MANIFEST="$REPO_ROOT/.context/cache/graph-manifest.json"
 EMBED_MANIFEST="$REPO_ROOT/.context/embeddings/manifest.json"
 
 if [[ ! -f "$MANIFEST" ]]; then
   echo "[status] No ingest manifest found."
-  echo "[status] Run: ./scripts/context.sh ingest"
+  echo "[status] Run: cortex ingest"
   exit 0
 fi
 
@@ -47,7 +48,7 @@ console.log(`[status] graph files=${c.files ?? 0} rules=${c.rules ?? 0} adrs=${c
 console.log(`[status] graph rels constrains=${c.constrains ?? 0} implements=${c.implements ?? 0} supersedes=${c.supersedes ?? 0}`);
 ' "$GRAPH_MANIFEST"
 else
-  echo "[status] graph manifest missing (run: ./scripts/context.sh graph-load)"
+  echo "[status] graph manifest missing (run: cortex graph-load)"
 fi
 
 if [[ -f "$EMBED_MANIFEST" ]]; then
@@ -68,13 +69,13 @@ if (embedded > 0 && output > 0 && failed === 0) {
 } else if (embedded > 0 && output > 0) {
   console.log(`[status] semantic_search=embedding+lexical-partial (failed=${failed})`);
 } else if (entities > 0) {
-  console.log("[status] semantic_search=lexical-only (run: ./scripts/context.sh embed)");
+  console.log("[status] semantic_search=lexical-only (run: cortex embed)");
 } else {
   console.log("[status] semantic_search=lexical-only (no indexed entities)");
 }
 ' "$EMBED_MANIFEST"
 else
-  echo "[status] embeddings manifest missing (run: ./scripts/context.sh embed)"
+  echo "[status] embeddings manifest missing (run: cortex embed)"
   echo "[status] semantic_search=lexical-only (embeddings manifest missing)"
 fi
 

package/scaffold/scripts/update-context.sh

@@ -1,18 +1,18 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 echo "[update] ingesting changed files"
-"$REPO_ROOT/scripts/ingest.sh" --changed
+"$SCRIPT_DIR/ingest.sh" --changed
 
 echo "[update] embedding changed entities"
-if ! "$REPO_ROOT/scripts/embed.sh" --changed; then
+if ! "$SCRIPT_DIR/embed.sh" --changed; then
   echo "[update] warning: embedding generation failed; continuing with lexical search fallback"
 fi
 
 echo "[update] rebuilding graph"
-"$REPO_ROOT/scripts/load-ryu.sh"
+"$SCRIPT_DIR/load-ryu.sh"
 
 echo "[update] status"
-"$REPO_ROOT/scripts/status.sh"
+"$SCRIPT_DIR/status.sh"

package/scaffold/scripts/watch.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 WATCH_DIR="$REPO_ROOT/.context/watch"
 PID_FILE="$WATCH_DIR/watch.pid"
 STAMP_FILE="$WATCH_DIR/last-stamp.sha1"
@@ -21,7 +22,7 @@ EVENT_BACKEND=""
 
 print_usage() {
   cat <<'USAGE'
-Usage: ./scripts/watch.sh [start|stop|status|run|once] [--interval <sec>] [--debounce <sec>] [--mode <auto|event|poll>]
+Usage: cortex watch [start|stop|status|run|once] [--interval <sec>] [--debounce <sec>] [--mode <auto|event|poll>]
 
 Commands:
   start     Start background watch loop
@@ -149,8 +150,8 @@ status_digest() {
   # .context/ excludes the relocated .context/mcp/ tree as well.
   find "$REPO_ROOT" -type f \
     ! -path "$REPO_ROOT/.context/*" \
-    ! -path "$REPO_ROOT/scripts/parsers/node_modules/*" \
-    ! -path "$REPO_ROOT/scripts/parsers/.npm-cache/*" \
+    ! -path "$REPO_ROOT/.context/scripts/parsers/node_modules/*" \
+    ! -path "$REPO_ROOT/.context/scripts/parsers/.npm-cache/*" \
     -print \
     | LC_ALL=C sort \
     | shasum -a 1 \
@@ -162,7 +163,7 @@ run_update() {
   start_ts="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
   echo "[watch] update start at $start_ts"
 
-  if bash "$REPO_ROOT/scripts/context.sh" update; then
+  if bash "$SCRIPT_DIR/context.sh" update; then
     echo "[watch] update success"
     return 0
   fi
@@ -199,15 +200,13 @@ wait_for_change_event() {
     inotifywait)
       inotifywait -q -r \
         -e modify,create,delete,move \
-        --exclude '(^|/)\\.git(/|$)|(^|/)\\.context(/|$)|(^|/)scripts/parsers/(node_modules|\\.npm-cache)(/|$)' \
+        --exclude '(^|/)\\.git(/|$)|(^|/)\\.context(/|$)' \
         "$REPO_ROOT" >/dev/null 2>&1 || true
       ;;
     fswatch)
       fswatch -1 -r \
         --exclude '(^|/)\\.git(/|$)' \
         --exclude '(^|/)\\.context(/|$)' \
-        --exclude '(^|/)scripts/parsers/node_modules(/|$)' \
-        --exclude '(^|/)scripts/parsers/\\.npm-cache(/|$)' \
         "$REPO_ROOT" >/dev/null 2>&1 || true
       ;;
     *)