create-academic-research 0.1.11 → 0.1.13

package/README.md

@@ -1,8 +1,19 @@
 # Create Academic Research
 
+[![npm](https://img.shields.io/npm/v/create-academic-research)](https://www.npmjs.com/package/create-academic-research)
+[![Validate](https://github.com/VincenzoImp/create-academic-research/actions/workflows/validate.yml/badge.svg)](https://github.com/VincenzoImp/create-academic-research/actions/workflows/validate.yml)
+[![Release](https://github.com/VincenzoImp/create-academic-research/actions/workflows/release.yml/badge.svg)](https://github.com/VincenzoImp/create-academic-research/actions/workflows/release.yml)
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+
 Create agent-ready academic research repositories with one command.
 
-From the npm registry:
+`create-academic-research` scaffolds a serious research workspace: source
+ledgers, SOTA files, citation audit tables, experiment records, reproducibility
+docs, durable wiki/log memory, project-local skills, and MCP setup for scholarly
+search. The template is discipline-general and especially strong for computer
+science research.
+
+## Quickstart
 
 ```bash
 npm create academic-research@latest my-project
@@ -23,9 +34,16 @@ From GitHub:
 npx --yes github:VincenzoImp/create-academic-research my-project
 ```
 
-The generator creates a complete research repository, personalizes the project
-name and Python package, configures project-local skills, writes MCP records,
-and prepares a durable wiki/log structure for agentic academic work.
+## What It Creates
+
+| Area | Generated Support |
+|---|---|
+| Sources | PDFs, derived Markdown, metadata, BibTeX, conversion ledger, source ledger. |
+| Literature Review | Search strategy, screening decisions, literature matrix, SOTA synthesis, gaps, PRISMA flow. |
+| Agent Memory | `AGENTS.md`, capability profile, MCP setup docs, generated MCP snippets, wiki index/log/templates. |
+| Reproducibility | Python package scaffold, tests, experiment registry, output folders, artifact checklist. |
+| Skills | Project-local installation flow for `VincenzoImp/academic-research-skills`. |
+| MCP | Conservative default records for scholarly discovery plus documented optional integrations. |
 
 The wizard is discipline-general: it creates a clean structure for academic
 research projects in any field. Its companion skill stack gives first-class
@@ -37,9 +55,18 @@ The generated repository is agent-neutral. By default the wizard records
 `agent: universal`, installs one shared project-local `.agents/skills` copy,
 and writes generic MCP snippets. Use `--agent <id>` only when you want to force
 a specific target recognized by the `skills` CLI. Run
-`npx academic-research agents list` inside a generated project to see every
+`npm run agents:list` inside a generated project to see every
 supported target and alias.
 
+## When To Use It
+
+Use this when starting or cleaning up an academic research project that needs
+evidence tracking, literature-review discipline, repeatable experiments, paper
+writing support, or LLM-agent collaboration. It is not a paper generator and it
+does not replace methodological judgment; it gives the repository enough
+structure for serious research work to compound instead of scattering across
+chat history, notebooks, PDFs, and ad hoc folders.
+
 ## Default Experience
 
 By default, the wizard:
@@ -86,35 +113,38 @@ npx create-academic-research@latest my-project --yes --no-install-skills
 Inside a generated project:
 
 ```bash
-npx academic-research doctor
-npx academic-research setup
-npx academic-research rename --title "New Title" --slug new-title --package new_title
-npx academic-research agents list
-npx academic-research skills presets
-npx academic-research skills install --preset default
-npx academic-research skills install --preset enhanced
-npx academic-research skills install source-ingestion sota-literature-review
-npx academic-research skills list
-npx academic-research skills status
-npx academic-research skills remove source-ingestion
-npx academic-research skills uninstall source-ingestion
-npx academic-research skills update
-npx academic-research mcp list
-npx academic-research mcp enabled
-npx academic-research mcp available
-npx academic-research mcp commands arxiv
-npx academic-research mcp env openalex semantic-scholar zotero
-npx academic-research mcp env --dotenv --all > .env.example
-npx academic-research mcp env --write .env.example --all
-npx academic-research mcp enable arxiv dblp
-npx academic-research mcp disable arxiv
-npx academic-research mcp install arxiv
-npx academic-research mcp uninstall arxiv
-npx academic-research mcp smoke --env-file .env.local
-npx academic-research mcp doctor --env-file .env.local
-npx academic-research mcp probe arxiv --timeout-ms 5000
+npm run doctor
+npm run setup
+npm run rename -- --title "New Title" --slug new-title --package new_title
+npm run agents:list
+npm run skills:presets
+npm run skills:install
+npm run skills:install -- --preset enhanced
+npm run skills:install -- source-ingestion sota-literature-review
+npm run skills:list
+npm run skills:status
+npm run skills:remove -- source-ingestion
+npm run skills:uninstall -- source-ingestion
+npm run skills:update
+npm run mcp:list
+npm run mcp:enabled
+npm run mcp:available
+npm run mcp:commands -- arxiv
+npm run mcp:env -- openalex semantic-scholar zotero
+npm run mcp:env -- --dotenv --all > .env.example
+npm run mcp:dotenv
+npm run mcp:enable -- arxiv dblp
+npm run mcp:disable -- arxiv
+npm run mcp:install -- arxiv
+npm run mcp:uninstall -- arxiv
+npm run mcp:smoke -- --env-file .env.local
+npm run mcp:doctor -- --env-file .env.local
+npm run mcp:probe -- arxiv --timeout-ms 5000
 ```
 
+For direct one-off invocation without the generated package scripts, use
+`npx --yes --package create-academic-research@latest academic-research <command>`.
+
 ## Command Model
 
 `academic-research setup` is a non-destructive onboarding status command. It
@@ -162,7 +192,7 @@ Those skills are portable `SKILL.md` instructions, but they require an
 agent/runtime that can load skills or include the relevant instructions in
 context. They are not automatic capabilities of every raw model API.
 Use `--agent <id>` for explicit setup with any id from
-`academic-research agents list`. The shorthand `--agent claude` is normalized
+`npm run agents:list`. The shorthand `--agent claude` is normalized
 to the supported `claude-code` target.
 Avoid `--agent auto` for unattended setup: the upstream `skills` CLI may expand
 it to every agent it detects on the machine.
@@ -181,9 +211,9 @@ Preset intent:
 MCP defaults are intentionally conservative. Semantic Scholar, OpenAlex,
 Zotero, Overleaf, Crossref, and fallback aggregators are useful, but they need
 API keys, local apps, manual setup, or source-policy review. Enable them with
-`npx academic-research mcp enable <server>` after reading
-`docs/agent/mcp-setup.md`, use `npx academic-research mcp env <server>` to see
-runtime prerequisites, then run `npx academic-research mcp doctor`.
+`npm run mcp:enable -- <server>` after reading
+`docs/agent/mcp-setup.md`, use `npm run mcp:env -- <server>` to see runtime
+prerequisites, then run `npm run mcp:doctor`.
 
 The MCP catalog distinguishes local runtime adapters from hosted endpoints and
 manual integrations. arXiv and DBLP are low-friction local `uvx` runtimes.
@@ -198,8 +228,8 @@ until a project explicitly needs them.
 
 Generated projects include a committed `.env.example` with empty MCP variables
 and ignore filled `.env` or `.env.local` files. Regenerate the example with
-`mcp env --write .env.example --all`. `mcp doctor`, `mcp smoke`, and
-`mcp probe` check the current process environment unless you explicitly pass
+`npm run mcp:dotenv`. `mcp doctor`, `mcp smoke`, and `mcp probe` check the
+current process environment unless you explicitly pass
 `--env-file .env.local`.
 
 Generated MCP snippets are project documentation and client-ready config, not
@@ -229,8 +259,8 @@ Releases are tag-driven. Update `package.json` and `package-lock.json`, commit
 the change, create `vX.Y.Z`, and push the tag:
 
 ```bash
-git tag -a v0.1.11 -m "v0.1.11"
-git push origin main v0.1.11
+git tag -a vX.Y.Z -m "vX.Y.Z"
+git push origin main vX.Y.Z
 ```
 
 Once the GitHub repository is public, the release workflow validates the tag

package/dist/src/agents.js

@@ -79,7 +79,7 @@ export function assertKnownAgentTarget(agent) {
         throw new Error([
             `unknown agent target: ${value}`,
             `Use ${DEFAULT_AGENT}, ${AUTO_AGENT}, or one supported skills.sh agent id.`,
-            "List targets with: npx -p create-academic-research academic-research agents list",
+            "List targets with: npx --yes --package create-academic-research@latest academic-research agents list",
             `Supported ids: ${specificAgentTargets().join(", ")}`,
             `Aliases: ${formatAgentAliasesInline()}`
         ].join("\n"));

package/dist/src/capabilities.js

@@ -331,12 +331,12 @@ async function writeCapabilityProfile(root, state) {
         "",
         "## Skills",
         "",
-        `- Install with: \`academic-research skills install --preset ${state.preset ?? "default"}\``,
-        "- Install selected skills with: `academic-research skills install <skill-id> [...]`",
-        "- List installed with: `academic-research skills list`",
-        "- List presets with: `academic-research skills presets`",
-        "- Remove with: `academic-research skills remove <skill>`",
-        "- Update with: `academic-research skills update`",
+        `- Install with: \`npm run skills:install -- --preset ${state.preset ?? "default"}\``,
+        "- Install selected skills with: `npm run skills:install -- <skill-id> [...]`",
+        "- List installed with: `npm run skills:list`",
+        "- List presets with: `npm run skills:presets`",
+        "- Remove with: `npm run skills:remove -- <skill>`",
+        "- Update with: `npm run skills:update`",
         "",
         "## MCP Servers",
         ""
@@ -383,7 +383,7 @@ async function writeMcpSetup(root, state) {
         lines.push(`- \`${name}\` (${status}, ${server.readiness}, ${server.priority}): ${server.source_need}`, `  - Source: \`${server.source}\``, `  - Execution mode: \`${server.execution_mode}\``, ...(server.hosted_url ? [`  - Hosted endpoint: <${server.hosted_url}>`] : []), ...server.setup_commands.map((command) => `  - Setup command: \`${command}\``));
         appendMcpPrerequisiteLines(lines, server.required_env, server.recommended_env, server.local_service);
     }
-    lines.push("", "## Operating Rules", "", "- Use `.env.example` as a committed reference and put filled secrets in `.env.local`, your shell, or your MCP client secret store.", "- Print a dotenv-style reference with `npx academic-research mcp env --dotenv --all`.", "- Regenerate a dotenv-style reference with `npx academic-research mcp env --write .env.example --all`.", "- Pass `--env-file .env.local` to `mcp doctor`, `mcp smoke`, or `mcp probe` when you want the CLI to read explicit local secrets.", "- Keep secrets in your shell, MCP client secret store, or local untracked files; do not commit tokens or API keys.", "- Prefer the smallest enabled MCP set that covers the current research question.", "- Treat MCP output as retrieval metadata. Promote claims into repository source records only after source ingestion and citation audit.", "- Run `npx academic-research mcp doctor` after changing MCP records or environment variables.", "- Run `npx academic-research mcp probe <server>` only when you intentionally want to start selected MCP server processes.", "");
+    lines.push("", "## Operating Rules", "", "- Use `.env.example` as a committed reference and put filled secrets in `.env.local`, your shell, or your MCP client secret store.", "- Print a dotenv-style reference with `npm run mcp:env -- --dotenv --all`.", "- Regenerate a dotenv-style reference with `npm run mcp:dotenv`.", "- Pass `--env-file .env.local` to `mcp doctor`, `mcp smoke`, or `mcp probe` when you want the CLI to read explicit local secrets.", "- Keep secrets in your shell, MCP client secret store, or local untracked files; do not commit tokens or API keys.", "- Prefer the smallest enabled MCP set that covers the current research question.", "- Treat MCP output as retrieval metadata. Promote claims into repository source records only after source ingestion and citation audit.", "- Run `npm run mcp:doctor` after changing MCP records or environment variables.", "- Run `npm run mcp:probe -- <server>` only when you intentionally want to start selected MCP server processes.", "");
     await mkdir(join(root, "docs/agent"), { recursive: true });
     await writeFile(join(root, "docs/agent/mcp-setup.md"), lines.join("\n"), "utf8");
 }

package/dist/src/cli.js

@@ -94,7 +94,7 @@ async function createMain(argv) {
         await installMcpTools(result.root, presetMcpServers(answers.preset));
     }
     console.log(`Created ${result.slug} at ${result.root}`);
-    console.log("Next: cd into the project and run `npx academic-research doctor`.");
+    console.log("Next: cd into the project and run `npm run doctor`.");
     return 0;
 }
 async function askInteractiveCreateOptions(defaults, locks) {
@@ -167,14 +167,14 @@ async function setupCommand(argv) {
     }
     console.log("");
     console.log("Next Commands");
-    console.log(`academic-research skills install --preset ${state.preset}`);
-    console.log("academic-research skills status");
-    console.log("academic-research mcp list");
-    console.log("academic-research mcp env");
-    console.log("academic-research mcp env --write .env.example --all");
-    console.log("academic-research mcp smoke");
-    console.log("academic-research mcp probe arxiv");
-    console.log("academic-research doctor");
+    console.log(`npm run skills:install -- --preset ${state.preset}`);
+    console.log("npm run skills:status");
+    console.log("npm run mcp:list");
+    console.log("npm run mcp:env");
+    console.log("npm run mcp:dotenv");
+    console.log("npm run mcp:smoke");
+    console.log("npm run mcp:probe -- arxiv");
+    console.log("npm run doctor");
     return project.ok ? 0 : 1;
 }
 async function renameCommand(argv) {
@@ -579,10 +579,10 @@ export function formatInteractiveCreateGuide() {
         "  default enables only low-friction arXiv; credentialed/local services are opt-in.",
         "  MCP installers are optional and run only finite installer commands.",
         "  MCP execution modes are explicit: uvx-runtime, npx-runtime, local-service, manual, or fallback.",
-        "  Use `academic-research mcp env <server>` to inspect env vars and local prerequisites.",
-        "  Use `academic-research mcp env --dotenv --all` to print a committed env example.",
-        "  Use `academic-research mcp env --write .env.example --all` to regenerate a committed env example.",
-        "  Use `academic-research mcp doctor --env-file .env.local` to check explicit local secrets.",
+        "  Use `npm run mcp:env -- <server>` to inspect env vars and local prerequisites.",
+        "  Use `npm run mcp:env -- --dotenv --all` to print a committed env example.",
+        "  Use `npm run mcp:dotenv` to regenerate a committed env example.",
+        "  Use `npm run mcp:doctor -- --env-file .env.local` to check explicit local secrets.",
         ""
     ].join("\n");
 }

package/dist/src/project.js

@@ -223,12 +223,54 @@ async function writeGeneratedPackageJson(root, { slug, preserveExistingSpec = fa
         (preserveExistingSpec ? existingSpec : undefined) ??
         await currentPackageVersion();
     data.name = slug;
+    data.scripts = {
+        ...(data.scripts ?? {}),
+        ...generatedLifecycleScripts(packageSpec)
+    };
     data.devDependencies = {
         ...(data.devDependencies ?? {}),
         "create-academic-research": packageSpec
     };
     await writeJson(path, data);
 }
+function generatedLifecycleScripts(packageSpec) {
+    const command = `npm exec --yes --package=${lifecyclePackageSpec(packageSpec)} -- academic-research`;
+    return {
+        doctor: `${command} doctor`,
+        setup: `${command} setup`,
+        rename: `${command} rename`,
+        "agents:list": `${command} agents list`,
+        "skills:install": `${command} skills install`,
+        "skills:list": `${command} skills list`,
+        "skills:status": `${command} skills status`,
+        "skills:presets": `${command} skills presets`,
+        "skills:remove": `${command} skills remove`,
+        "skills:uninstall": `${command} skills uninstall`,
+        "skills:update": `${command} skills update`,
+        "mcp:list": `${command} mcp list`,
+        "mcp:enabled": `${command} mcp enabled`,
+        "mcp:available": `${command} mcp available`,
+        "mcp:commands": `${command} mcp commands`,
+        "mcp:env": `${command} mcp env`,
+        "mcp:dotenv": `${command} mcp env --write .env.example --all`,
+        "mcp:enable": `${command} mcp enable`,
+        "mcp:disable": `${command} mcp disable`,
+        "mcp:install": `${command} mcp install`,
+        "mcp:uninstall": `${command} mcp uninstall`,
+        "mcp:smoke": `${command} mcp smoke`,
+        "mcp:doctor": `${command} mcp doctor`,
+        "mcp:probe": `${command} mcp probe`
+    };
+}
+function lifecyclePackageSpec(packageSpec) {
+    if (packageSpec === "create-academic-research" || packageSpec.startsWith("create-academic-research@")) {
+        return packageSpec;
+    }
+    if (/^(file:|github:|git[+:]|https?:)/.test(packageSpec) || packageSpec.includes("/")) {
+        return packageSpec;
+    }
+    return `create-academic-research@${packageSpec}`;
+}
 async function writeGeneratedGitignore(root) {
     const source = join(root, "_gitignore");
     if (await exists(source)) {

package/package.json

@@ -1,17 +1,24 @@
 {
   "name": "create-academic-research",
-  "version": "0.1.11",
-  "description": "Create and manage agent-ready academic research repositories.",
+  "version": "0.1.13",
+  "description": "Scaffold agent-ready academic research repositories with SOTA, source ledgers, wiki memory, MCP setup, and project-local skills.",
   "type": "module",
   "license": "MIT",
   "author": "Vincenzo Imperati",
   "keywords": [
     "academic-research",
+    "academic-writing",
+    "arxiv",
+    "citation-management",
     "research-project",
+    "research-scaffold",
     "agent-skills",
+    "llm-agents",
     "mcp",
     "literature-review",
-    "reproducibility"
+    "open-science",
+    "reproducibility",
+    "sota"
   ],
   "repository": {
     "type": "git",

package/template/README.md

@@ -30,7 +30,7 @@ python3.11 -m venv .venv
 source .venv/bin/activate
 python -m pip install --upgrade pip
 python -m pip install -e ".[dev]"
-npx academic-research doctor
+npm run doctor
 ```
 
 ## Core Folders
@@ -53,23 +53,23 @@ npx academic-research doctor
 Project-local skills and MCP records are managed with:
 
 ```bash
-npx academic-research skills presets
-npx academic-research agents list
-npx academic-research skills install --preset default
-npx academic-research skills install --preset enhanced
-npx academic-research skills install source-ingestion sota-literature-review
-npx academic-research skills list
-npx academic-research skills status
-npx academic-research setup
-npx academic-research mcp env --write .env.example --all
-npx academic-research mcp list
-npx academic-research mcp env openalex semantic-scholar zotero
-npx academic-research mcp enable arxiv dblp
-npx academic-research mcp commands arxiv
-npx academic-research mcp install arxiv
-npx academic-research mcp smoke --env-file .env.local
-npx academic-research mcp doctor --env-file .env.local
-npx academic-research mcp probe arxiv --timeout-ms 5000
+npm run skills:presets
+npm run agents:list
+npm run skills:install
+npm run skills:install -- --preset enhanced
+npm run skills:install -- source-ingestion sota-literature-review
+npm run skills:list
+npm run skills:status
+npm run setup
+npm run mcp:dotenv
+npm run mcp:list
+npm run mcp:env -- openalex semantic-scholar zotero
+npm run mcp:enable -- arxiv dblp
+npm run mcp:commands -- arxiv
+npm run mcp:install -- arxiv
+npm run mcp:smoke -- --env-file .env.local
+npm run mcp:doctor -- --env-file .env.local
+npm run mcp:probe -- arxiv --timeout-ms 5000
 ```
 
 `skills list` reports installed project-local skills. `skills presets` reports
@@ -81,10 +81,10 @@ commands; runtime-only `uvx`/`npx` MCP servers may have no install step and are
 started later by the MCP client.
 
 `.env.example` is the committed MCP environment reference. Regenerate it with
-`mcp env --write .env.example --all`. Copy it to `.env.local`, your shell
-profile, or your MCP client secret store when secrets are needed. Filled `.env`
-files are ignored by git. `mcp doctor` checks the current process environment
-unless you explicitly pass `--env-file .env.local`.
+`npm run mcp:dotenv`. Copy it to `.env.local`, your shell profile, or your MCP
+client secret store when secrets are needed. Filled `.env` files are ignored by
+git. `mcp doctor` checks the current process environment unless you explicitly
+pass `--env-file .env.local`.
 
 `setup` prints the current project capability state, installed skill counts,
 enabled MCP records, and the next onboarding commands without changing files.

package/template/docs/agent/mcp-client-setup.md

@@ -19,7 +19,7 @@ store.
 Regenerate the committed reference from the current MCP catalog with:
 
 ```bash
-npx academic-research mcp env --write .env.example --all
+npm run mcp:dotenv
 ```
 
 Create a private local file when needed:
@@ -33,9 +33,9 @@ Do not commit filled `.env`, `.env.local`, tokens, cookies, or browser sessions.
 environment unless you explicitly pass `--env-file .env.local`.
 
 ```bash
-npx academic-research mcp doctor --env-file .env.local
-npx academic-research mcp smoke --env-file .env.local
-npx academic-research mcp probe arxiv --timeout-ms 5000
+npm run mcp:doctor -- --env-file .env.local
+npm run mcp:smoke -- --env-file .env.local
+npm run mcp:probe -- arxiv --timeout-ms 5000
 ```
 
 ## Client Notes
@@ -57,10 +57,10 @@ required variables are already exported.
 ## Workflow
 
 1. Enable only the MCP servers needed for the current research task.
-2. Inspect prerequisites with `npx academic-research mcp env <server>`.
+2. Inspect prerequisites with `npm run mcp:env -- <server>`.
 3. Put required secrets in the MCP client secret store, shell, or `.env.local`.
-4. Run `npx academic-research mcp smoke --env-file .env.local`.
-5. Run `npx academic-research mcp probe <server>` only when you want to start
+4. Run `npm run mcp:smoke -- --env-file .env.local`.
+5. Run `npm run mcp:probe -- <server>` only when you want to start
    the server and verify a real stdio handshake.
 6. Load the generated snippet in the MCP client.
 7. Treat MCP output as retrieval metadata until it is ingested into repository

package/template/docs/agent/mcp-setup.md

@@ -5,9 +5,8 @@ and known risks here.
 
 Use `.env.example` as the committed environment reference. Put filled values in
 `.env.local`, the shell, or the MCP client secret store. Regenerate the example
-with `npx academic-research mcp env --write .env.example --all`.
+with `npm run mcp:dotenv`.
 
-Use `npx academic-research mcp doctor --env-file .env.local` when you want the
-CLI to read an explicit local env file. Use `npx academic-research mcp probe
-<server>` only when you want to start a selected MCP server and verify a real
-stdio handshake.
+Use `npm run mcp:doctor -- --env-file .env.local` when you want the CLI to read
+an explicit local env file. Use `npm run mcp:probe -- <server>` only when you
+want to start a selected MCP server and verify a real stdio handshake.

package/template/docs/getting-started.md

@@ -6,8 +6,8 @@ Use this path for the first working session in a new research repository.
 
 ```bash
 npm install
-npx academic-research doctor
-npx academic-research setup
+npm run doctor
+npm run setup
 ```
 
 `doctor` checks required files and structural contracts. `setup` prints the
@@ -19,15 +19,15 @@ commands without changing files.
 Install the default academic research skill package:
 
 ```bash
-npx academic-research skills install --preset default
-npx academic-research skills status
+npm run skills:install
+npm run skills:status
 ```
 
 Use `enhanced` only when the project also needs complementary development,
 document, frontend, testing, and conversion skills:
 
 ```bash
-npx academic-research skills install --preset enhanced
+npm run skills:install -- --preset enhanced
 ```
 
 ## 3. Prepare MCP Environment
@@ -36,18 +36,18 @@ Keep `.env.example` committed and empty of real secrets. Put filled values in
 `.env.local`, your shell, or your MCP client secret store.
 
 ```bash
-npx academic-research mcp env --write .env.example --all
+npm run mcp:dotenv
 cp .env.example .env.local
-npx academic-research mcp env openalex semantic-scholar zotero
-npx academic-research mcp doctor --env-file .env.local
+npm run mcp:env -- openalex semantic-scholar zotero
+npm run mcp:doctor -- --env-file .env.local
 ```
 
 `mcp smoke` is a non-launching readiness check. `mcp probe` is opt-in and starts
 MCP processes for a real stdio handshake.
 
 ```bash
-npx academic-research mcp smoke --env-file .env.local
-npx academic-research mcp probe arxiv --timeout-ms 5000
+npm run mcp:smoke -- --env-file .env.local
+npm run mcp:probe -- arxiv --timeout-ms 5000
 ```
 
 ## 4. Start Source Work

package/template/package.json

@@ -3,20 +3,32 @@
   "private": true,
   "type": "module",
   "scripts": {
-    "doctor": "academic-research doctor",
-    "setup": "academic-research setup",
-    "skills:install": "academic-research skills install --preset default",
-    "skills:list": "academic-research skills list",
-    "skills:presets": "academic-research skills presets",
-    "mcp:list": "academic-research mcp list",
-    "mcp:commands": "academic-research mcp commands",
-    "mcp:env": "academic-research mcp env",
-    "mcp:dotenv": "academic-research mcp env --write .env.example --all",
-    "mcp:smoke": "academic-research mcp smoke",
-    "mcp:doctor": "academic-research mcp doctor",
-    "mcp:probe": "academic-research mcp probe"
+    "doctor": "npm exec --yes --package=create-academic-research@latest -- academic-research doctor",
+    "setup": "npm exec --yes --package=create-academic-research@latest -- academic-research setup",
+    "rename": "npm exec --yes --package=create-academic-research@latest -- academic-research rename",
+    "agents:list": "npm exec --yes --package=create-academic-research@latest -- academic-research agents list",
+    "skills:install": "npm exec --yes --package=create-academic-research@latest -- academic-research skills install",
+    "skills:list": "npm exec --yes --package=create-academic-research@latest -- academic-research skills list",
+    "skills:status": "npm exec --yes --package=create-academic-research@latest -- academic-research skills status",
+    "skills:presets": "npm exec --yes --package=create-academic-research@latest -- academic-research skills presets",
+    "skills:remove": "npm exec --yes --package=create-academic-research@latest -- academic-research skills remove",
+    "skills:uninstall": "npm exec --yes --package=create-academic-research@latest -- academic-research skills uninstall",
+    "skills:update": "npm exec --yes --package=create-academic-research@latest -- academic-research skills update",
+    "mcp:list": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp list",
+    "mcp:enabled": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp enabled",
+    "mcp:available": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp available",
+    "mcp:commands": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp commands",
+    "mcp:env": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp env",
+    "mcp:dotenv": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp env --write .env.example --all",
+    "mcp:enable": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp enable",
+    "mcp:disable": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp disable",
+    "mcp:install": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp install",
+    "mcp:uninstall": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp uninstall",
+    "mcp:smoke": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp smoke",
+    "mcp:doctor": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp doctor",
+    "mcp:probe": "npm exec --yes --package=create-academic-research@latest -- academic-research mcp probe"
   },
   "devDependencies": {
-    "create-academic-research": "0.1.11"
+    "create-academic-research": "0.1.13"
   }
 }