create-academic-research 0.1.1 → 0.1.3

package/README.md

@@ -14,6 +14,9 @@ Equivalent explicit form:
 npx create-academic-research@latest my-project
 ```
 
+Prefer the explicit `@latest` form. Some npm/npx versions reuse an older
+cached creator when the version is omitted.
+
 From GitHub:
 
 ```bash
@@ -31,10 +34,10 @@ software engineering, databases, theory, robotics, IR, PL, graphics, and
 adjacent interdisciplinary CS.
 
 The generated repository is agent-neutral. By default the wizard records
-`agent: auto`, lets the `skills` CLI detect the current local agent, and writes
-generic MCP snippets. Use `--agent <name>` only when you want to force a
-specific target recognized by the `skills` CLI, such as `claude-code`,
-`cursor`, `windsurf`, or another supported local loader.
+`agent: universal`, installs one shared project-local `.agents/skills` copy,
+and writes generic MCP snippets. Use `--agent <name>` only when you want to
+force a specific target recognized by the `skills` CLI, such as `claude-code`,
+`codex`, `cursor`, `windsurf`, or another supported local loader.
 
 ## Default Experience
 
@@ -112,10 +115,10 @@ MCP commands are split by side-effect:
 | `mcp list` | List known MCP servers with enabled/available status. |
 | `mcp enabled` | List only enabled MCP server ids. |
 | `mcp available` | List the local MCP catalog. |
-| `mcp commands` | Print external install commands without running them. |
+| `mcp commands` | Print finite external install commands without running them. Runtime-only `uvx`/`npx` servers may have no install command. |
 | `mcp enable` | Enable an MCP server in project records and generated snippets. |
 | `mcp disable` | Remove an MCP server from project records and generated snippets. |
-| `mcp install` | Run the external tool install command for selected MCP servers. |
+| `mcp install` | Run finite external tool install commands for selected MCP servers. It must not launch stdio MCP servers. |
 | `mcp uninstall` | Run the external uninstall command when one exists. |
 | `mcp doctor` | Validate enabled MCP records and generated snippets. |
 
@@ -131,8 +134,10 @@ The create wizard can install that project-local package automatically.
 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 <agent>` for explicit multi-tool setup; reserve `--agent '*'` for
-cases where you intentionally want every local agent loader populated.
+Use `--agent <agent>` for explicit setup, for example `--agent codex` or
+`--agent claude-code`.
+Avoid `--agent auto` for unattended setup: the upstream `skills` CLI may expand
+it to every agent it detects on the machine.
 
 Preset intent:
 
@@ -161,8 +166,8 @@ 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 v0.1.1 -m "v0.1.1"
-git push origin main v0.1.1
+git tag -a v0.1.3 -m "v0.1.3"
+git push origin main v0.1.3
 ```
 
 Once the GitHub repository is public, the release workflow validates the tag

package/dist/src/capabilities.d.ts

@@ -1,6 +1,6 @@
 import { type Runner } from "./runner.js";
 import { type McpToolCommandKey } from "./stack.js";
-export declare const DEFAULT_AGENT = "auto";
+export declare const DEFAULT_AGENT = "universal";
 export interface CapabilityState {
     agent: string;
     preset: string;

package/dist/src/capabilities.js

@@ -3,7 +3,8 @@ import { join, relative } from "node:path";
 import YAML from "yaml";
 import { defaultRunner } from "./runner.js";
 import { AGENT_STACK, presetMcpServers } from "./stack.js";
-export const DEFAULT_AGENT = "auto";
+export const DEFAULT_AGENT = "universal";
+const AUTO_AGENT = "auto";
 export async function readCapabilities(root) {
     try {
         return readCapabilitiesFile(root);
@@ -293,7 +294,7 @@ async function writeCapabilityProfile(root, state) {
             lines.push(`- \`${name}\` (${status}): ${server?.smoke_test ?? "Smoke-test before use."}`);
         }
     }
-    lines.push("", "## Rules", "", "- Skill installation is project-local by default.", "- Agent target `auto` lets the local skills CLI detect the active agent.", "- MCP enable/disable changes project records; install/uninstall changes external tools.", "- Keep API keys, tokens, cookies, and browser sessions out of git.", "- Cite repository source records, not raw MCP output alone.", "");
+    lines.push("", "## Rules", "", "- Skill installation is project-local by default.", "- Agent target `universal` installs one shared project-local `.agents/skills` copy.", "- MCP enable/disable changes project records; install/uninstall changes external tools.", "- Keep API keys, tokens, cookies, and browser sessions out of git.", "- Cite repository source records, not raw MCP output alone.", "");
     await writeFile(join(root, "docs/agent/capability-profile.md"), lines.join("\n"), "utf8");
 }
 async function appendCapabilityLog(root, state) {
@@ -307,7 +308,7 @@ function dedupe(values) {
 }
 function renderSkillCommand(command, agent) {
     const normalized = normalizeAgent(agent);
-    const agentFlag = normalized === DEFAULT_AGENT ? "" : `--agent '${normalized}'`;
+    const agentFlag = normalized === AUTO_AGENT ? "" : `--agent '${normalized}'`;
     return command.replaceAll("{agent_flag}", agentFlag).replaceAll("{agent}", normalized);
 }
 async function readCapabilitiesFile(root) {
@@ -402,7 +403,7 @@ function normalizeAgent(agent) {
 }
 function mcpSnippetFileName(agent) {
     const normalized = normalizeAgent(agent);
-    return normalized === DEFAULT_AGENT ? "mcp.json" : `${normalized}-mcp.json`;
+    return normalized === DEFAULT_AGENT || normalized === AUTO_AGENT ? "mcp.json" : `${normalized}-mcp.json`;
 }
 async function removeInactiveMcpSnippets(outputDir, activeFile) {
     const entries = await readdir(outputDir);

package/dist/src/cli.js

@@ -224,7 +224,7 @@ async function mcpCommand(argv) {
         const enabled = new Set(state.mcp_servers ?? []);
         for (const [name, server] of Object.entries(AGENT_STACK.mcp_servers)) {
             const status = enabled.has(name) ? "enabled" : "available";
-            const installer = server.install_command || "manual";
+            const installer = mcpInstallMode(server.install_command, server.command);
             console.log(`${status}\t${name}\t${server.source_need}\t${installer}`);
         }
         return 0;
@@ -242,7 +242,7 @@ async function mcpCommand(argv) {
         assertOnlyOptions(parsed.flags, "mcp available", []);
         assertNoArguments(parsed.positionals, "mcp available");
         for (const [name, server] of Object.entries(AGENT_STACK.mcp_servers)) {
-            const installer = server.install_command || "manual";
+            const installer = mcpInstallMode(server.install_command, server.command);
             console.log(`${name}\t${server.source_need}\t${installer}`);
         }
         return 0;
@@ -383,6 +383,11 @@ function assertOnlyOptions(flags, command, allowedOptions) {
         throw new Error(`${command} does not accept ${unexpected.map((name) => `--${name}`).join(", ")}`);
     }
 }
+function mcpInstallMode(installCommand, runtimeCommand) {
+    if (installCommand)
+        return installCommand;
+    return runtimeCommand ? "runtime-only" : "manual";
+}
 function printCreateHelp() {
     console.log([
         "Usage: create-academic-research <project-name> [options]",
@@ -396,10 +401,10 @@ function printCreateHelp() {
         "  --package <name>         Python package name. Default: normalized project name.",
         "  --preset <name>           Capability preset: minimal, default, enhanced, literature, writing, full.",
         "  --profile <name>          Project profile metadata. Default: academic-general.",
-        "  --agent <name>            Agent target. Default: auto-detect.",
+        "  --agent <name>            Agent target. Default: universal.",
         "  --install-skills          Install project-local skills without prompting.",
         "  --no-install-skills       Skip project-local skill installation.",
-        "  --install-mcp-tools       Run external MCP install commands after creation.",
+        "  --install-mcp-tools       Run finite external MCP install commands after creation.",
         "  -h, --help               Show this help.",
         "  -v, --version            Show package version."
     ].join("\n"));
@@ -441,7 +446,7 @@ function printMcpHelp() {
     console.log([
         "Usage: academic-research mcp <list|enabled|available|commands|enable|disable|install|uninstall|doctor> [servers...]",
         "",
-        "Manage MCP records and explicit external MCP tool installs.",
+        "Manage MCP records and finite external MCP tool installs.",
         "",
         "Options:",
         "  --root <path>            Project root for project-state commands.",

package/dist/src/project.js

@@ -205,7 +205,7 @@ async function writeGeneratedPackageJson(root, { slug }) {
     const path = join(root, "package.json");
     const data = await readJson(path);
     const existingSpec = data.devDependencies?.["create-academic-research"];
-    const packageSpec = process.env.CREATE_ACADEMIC_RESEARCH_PACKAGE_SPEC ?? existingSpec ?? "^0.1.1";
+    const packageSpec = process.env.CREATE_ACADEMIC_RESEARCH_PACKAGE_SPEC ?? existingSpec ?? "^0.1.3";
     data.name = slug;
     data.devDependencies = {
         ...(data.devDependencies ?? {}),

package/dist/src/stack.js

@@ -112,7 +112,7 @@ export const AGENT_STACK = {
         "semantic-scholar": {
             priority: "default",
             source_need: "Semantic Scholar papers, citations, authors, and recommendations.",
-            install_command: "uvx --from git+https://github.com/akapet00/semantic-scholar-mcp semantic-scholar-mcp --help",
+            install_command: "",
             uninstall_command: "",
             command: "uvx",
             args: ["--from", "git+https://github.com/akapet00/semantic-scholar-mcp", "semantic-scholar-mcp"],
@@ -123,7 +123,7 @@ export const AGENT_STACK = {
         openalex: {
             priority: "default",
             source_need: "OpenAlex broad scholarly graph.",
-            install_command: "npx -y @cyanheads/openalex-mcp-server --help",
+            install_command: "",
             uninstall_command: "",
             command: "npx",
             args: ["-y", "@cyanheads/openalex-mcp-server"],
@@ -145,7 +145,7 @@ export const AGENT_STACK = {
         pubmed: {
             priority: "domain-specific",
             source_need: "PubMed and biomedical literature.",
-            install_command: "npx -y @cyanheads/pubmed-mcp-server --help",
+            install_command: "",
             uninstall_command: "",
             command: "npx",
             args: ["-y", "@cyanheads/pubmed-mcp-server"],
@@ -156,7 +156,7 @@ export const AGENT_STACK = {
         zotero: {
             priority: "local-library",
             source_need: "Zotero local library and attachments.",
-            install_command: "uvx zoty --help",
+            install_command: "",
             uninstall_command: "",
             command: "uvx",
             args: ["zoty", "mcp"],

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "create-academic-research",
-  "version": "0.1.1",
+  "version": "0.1.3",
   "description": "Create and manage agent-ready academic research repositories.",
   "type": "module",
   "license": "MIT",

package/template/README.md

@@ -16,7 +16,8 @@ actual discipline. The companion `academic-research-skills` package gives
 first-class support to computer science research while keeping the repository
 structure useful for broader academic work.
 
-The repository is agent-neutral. Capability state uses `agent: auto` unless a
+The repository is agent-neutral. Capability state uses `agent: universal` by
+default, which installs one shared project-local `.agents/skills` copy unless a
 specific agent target is selected with `--agent`.
 
 ## Quickstart
@@ -64,9 +65,9 @@ npx academic-research mcp install arxiv
 
 `skills list` reports installed project-local skills. `skills presets` reports
 available install presets. `mcp enable` changes project records. `mcp commands`
-prints external install commands without running them. `mcp install` runs
-external tool installation commands and should be used only after reviewing the
-selected MCP.
+prints finite external install commands without running them. `mcp install`
+runs only finite tool installation commands; runtime-only `uvx`/`npx` MCP
+servers may have no install step and are started later by the MCP client.
 
 `default` installs the companion academic research skill package and keeps the
 MCP records focused on core scholarly discovery. `enhanced` adds complementary

package/template/configs/capabilities.yaml

@@ -1,4 +1,4 @@
-agent: auto
+agent: universal
 preset: default
 scope: project-local
 mcp_servers: []

package/template/docs/agent/capability-profile.md

@@ -1,6 +1,6 @@
 # Agent Capability Profile
 
-- Agent target: `auto`
+- Agent target: `universal`
 - Scope: `project-local`
 
 This file is written during project creation.

package/template/package.json

@@ -12,6 +12,6 @@
     "mcp:doctor": "academic-research mcp doctor"
   },
   "devDependencies": {
-    "create-academic-research": "^0.1.1"
+    "create-academic-research": "^0.1.3"
   }
 }