create-academic-research 0.1.6 → 0.1.8

package/README.md

@@ -53,6 +53,9 @@ By default, the wizard:
 - writes `docs/agent/capability-profile.md`;
 - writes `docs/agent/mcp-setup.md`;
 - writes `docs/agent/generated/mcp.json` unless an explicit agent target is set;
+- includes `scripts/README.md` for repeatable command entrypoints;
+- includes reusable `wiki/templates/` pages for sources, claims, experiments,
+  decisions, reviewer concerns, and research questions;
 - appends the onboarding event to `wiki/log.md`;
 - does not install external MCP tools unless explicitly requested.
 
@@ -84,11 +87,13 @@ 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
@@ -99,21 +104,26 @@ 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 enable arxiv openalex
+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
 npx academic-research mcp doctor
 ```
 
 ## Command Model
 
+`academic-research setup` is a non-destructive onboarding status command. It
+prints the active preset, agent, skill counts, enabled MCP records, and next
+commands without changing files.
+
 Skills are project-local by default.
 
 | Command | Meaning |
 |---|---|
 | `skills presets` | List available capability presets. |
-| `skills install` | Install project-local skills for the selected preset and project agent. This does not change MCP records. |
+| `skills install` | Install project-local skills by preset, or selected skill ids such as `source-ingestion`. This does not change MCP records. |
 | `skills list` | List skills found in project-local skill loader directories. |
 | `skills status` | Show configured project preset, agent, scope, skill roots, unique skill ids, and installed copies. |
 | `skills remove` / `skills uninstall` | Remove selected project-local skills. |
@@ -132,6 +142,7 @@ MCP commands are split by side-effect:
 | `mcp disable` | Remove an MCP server from project records and generated snippets. |
 | `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 smoke` | Print non-launching readiness diagnostics for enabled or selected MCP servers. |
 | `mcp doctor` | Validate enabled MCP records, generated snippets, required env vars, and documented manual prerequisites. |
 
 ## Companion Skills
@@ -185,6 +196,9 @@ live tools by themselves. Your MCP client must load the generated snippet, and
 the referenced commands must be available on your machine or runnable through
 `uvx`/`npx`. `mcp install` only runs finite setup commands such as the arXiv
 tool install; it deliberately does not launch stdio MCP servers.
+Use `mcp smoke` for a non-launching readiness pass before wiring a client: it
+checks required env vars, manual/local-service status, and whether runtime
+commands are visible on `PATH`.
 
 ## Validate This Package
 
@@ -202,8 +216,8 @@ 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 v0.1.6 -m "v0.1.6"
-git push origin main v0.1.6
+git tag -a v0.1.8 -m "v0.1.8"
+git push origin main v0.1.8
 ```
 
 Once the GitHub repository is public, the release workflow validates the tag

package/dist/src/capabilities.d.ts

@@ -16,6 +16,7 @@ export interface InitializeCapabilitiesOptions {
 export interface CapabilityCommandResult {
     ok: true;
     count?: number;
+    skills?: string[];
     servers?: string[];
 }
 export interface InstalledSkill {
@@ -36,7 +37,9 @@ export declare function readCapabilities(root: string): Promise<CapabilityState>
 export declare function writeCapabilities(root: string, state: Partial<CapabilityState>): Promise<void>;
 export declare function initializeCapabilities(root: string, options?: InitializeCapabilitiesOptions): Promise<void>;
 export declare function buildSkillInstallCommands(root: string, preset?: string, options?: SkillInstallOptions): Promise<string[][]>;
+export declare function buildExplicitSkillInstallCommands(root: string, skills: string[], options?: SkillInstallOptions): Promise<string[][]>;
 export declare function installSkills(root: string, preset?: string, options?: SkillInstallOptions, runner?: Runner): Promise<CapabilityCommandResult>;
+export declare function installSkillIds(root: string, skills: string[], options?: SkillInstallOptions, runner?: Runner): Promise<CapabilityCommandResult>;
 export declare function listInstalledSkills(root: string): Promise<InstalledSkill[]>;
 export declare function removeSkills(root: string, skills: string[], runner?: Runner): Promise<CapabilityCommandResult>;
 export declare function updateSkills(root: string, runner?: Runner): Promise<CapabilityCommandResult>;

package/dist/src/capabilities.js

@@ -60,6 +60,21 @@ export async function buildSkillInstallCommands(root, preset = "default", option
     }
     return commands;
 }
+export async function buildExplicitSkillInstallCommands(root, skills, options = {}) {
+    const selectedSkills = normalizeSkillIds(skills);
+    const state = await readCapabilities(root);
+    const agent = assertKnownAgentTarget(options.agent ?? state.agent);
+    const skillsBySource = new Map();
+    for (const skill of selectedSkills) {
+        const source = skillSourceForId(skill);
+        if (!source)
+            throw new Error(`unknown skill id: ${skill}`);
+        const sourceSkills = skillsBySource.get(source) ?? [];
+        sourceSkills.push(skill);
+        skillsBySource.set(source, sourceSkills);
+    }
+    return [...skillsBySource.entries()].map(([source, sourceSkills]) => skillAddCommand(source, sourceSkills, agent));
+}
 export async function installSkills(root, preset = "default", options = {}, runner = defaultRunner) {
     const state = await readCapabilities(root);
     const agent = assertKnownAgentTarget(options.agent ?? state.agent);
@@ -76,6 +91,22 @@ export async function installSkills(root, preset = "default", options = {}, runn
     }
     return { ok: true, count: commands.length };
 }
+export async function installSkillIds(root, skills, options = {}, runner = defaultRunner) {
+    const state = await readCapabilities(root);
+    const agent = assertKnownAgentTarget(options.agent ?? state.agent);
+    const selectedSkills = normalizeSkillIds(skills);
+    const commands = await buildExplicitSkillInstallCommands(root, selectedSkills, options);
+    for (const command of commands) {
+        await runner.run(command, { cwd: root });
+    }
+    if (state.agent !== agent) {
+        await writeCapabilities(root, {
+            ...state,
+            agent
+        });
+    }
+    return { ok: true, count: commands.length, skills: selectedSkills };
+}
 export async function listInstalledSkills(root) {
     const roots = await discoverProjectSkillRoots(root);
     const skills = [];
@@ -287,6 +318,7 @@ async function writeCapabilityProfile(root, state) {
         "## Skills",
         "",
         `- Install with: \`academic-research skills install --preset ${state.preset ?? "default"}\``,
+        "- Install selected skills with: `academic-research skills install <skill-id> [...]`",
         "- List installed with: `academic-research skills list`",
         "- List presets with: `academic-research skills presets`",
         "- Remove with: `academic-research skills remove <skill>`",
@@ -355,6 +387,48 @@ function renderSkillCommand(command, agent) {
     const agentFlag = normalized === AUTO_AGENT ? "" : `--agent '${normalized}'`;
     return command.replaceAll("{agent_flag}", agentFlag).replaceAll("{agent}", normalized);
 }
+function skillAddCommand(source, skills, agent) {
+    return [
+        "npm",
+        "exec",
+        "--yes",
+        "--package",
+        "skills",
+        "--",
+        "skills",
+        "add",
+        source,
+        ...skillAgentArgs(agent),
+        "--skill",
+        ...skills,
+        "--copy",
+        "-y"
+    ];
+}
+function skillAgentArgs(agent) {
+    const normalized = assertKnownAgentTarget(agent);
+    return normalized === AUTO_AGENT ? [] : ["--agent", normalized];
+}
+function normalizeSkillIds(skills) {
+    if (skills.length === 0)
+        throw new Error("no skills selected");
+    const result = [];
+    for (const skill of skills) {
+        if (!/^[a-z0-9][a-z0-9._-]*$/.test(skill)) {
+            throw new Error(`invalid skill id: ${skill}`);
+        }
+        if (!result.includes(skill))
+            result.push(skill);
+    }
+    return result;
+}
+function skillSourceForId(skill) {
+    for (const source of Object.values(AGENT_STACK.skill_sources)) {
+        if (source.skills.includes(skill))
+            return source.source;
+    }
+    return undefined;
+}
 function appendMcpPrerequisiteLines(lines, requiredEnv, recommendedEnv, localService) {
     if (requiredEnv.length > 0)
         lines.push(`  - Requires env: ${requiredEnv.map((name) => `\`${name}\``).join(", ")}`);

package/dist/src/cli.js

@@ -1,7 +1,7 @@
-import { readFileSync } from "node:fs";
-import { basename, dirname, join, resolve } from "node:path";
+import { existsSync, readFileSync } from "node:fs";
+import { basename, delimiter, dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
-import { assertKnownMcpServers, disableMcpServers, doctorMcpServers, enableMcpServers, DEFAULT_AGENT, installMcpTools, installSkills, listInstalledSkills, mcpToolCommandTexts, readCapabilities, removeSkills, uninstallMcpTools, updateSkills } from "./capabilities.js";
+import { assertKnownMcpServers, disableMcpServers, doctorMcpServers, enableMcpServers, DEFAULT_AGENT, installMcpTools, installSkillIds, installSkills, listInstalledSkills, mcpToolCommandTexts, readCapabilities, removeSkills, uninstallMcpTools, updateSkills } from "./capabilities.js";
 import { createProject, doctorProject, renameProject } from "./project.js";
 import { askCreateOptions } from "./prompts.js";
 import { AGENT_STACK, presetMcpServers } from "./stack.js";
@@ -9,7 +9,15 @@ import { formatAgentAliasLines, formatAgentTargetList, formatSupportedAgentTarge
 import { packageify, slugify, titleFromSlug } from "./names.js";
 const packageRoot = resolve(dirname(fileURLToPath(import.meta.url)), "../..");
 const packageVersion = readPackageVersion();
-const CREATE_FLAGS = flagSchema(["yes", "help", "version", "install-skills", "no-install-skills", "install-mcp-tools"], ["title", "slug", "package", "preset", "profile", "agent"]);
+const CREATE_FLAGS = flagSchema([
+    "yes",
+    "help",
+    "version",
+    "install-skills",
+    "no-install-skills",
+    "install-mcp-tools",
+    "no-install-mcp-tools"
+], ["title", "slug", "package", "preset", "profile", "agent"]);
 const ROOT_FLAGS = flagSchema(["help"], ["root"]);
 const RENAME_FLAGS = flagSchema(["help"], ["root", "title", "slug", "package"]);
 const SKILLS_FLAGS = flagSchema(["help"], ["root", "preset", "agent"]);
@@ -43,6 +51,9 @@ async function createMain(argv) {
     if (flagBool(parsed.flags, "install-skills") && flagBool(parsed.flags, "no-install-skills")) {
         throw new Error("cannot use --install-skills and --no-install-skills together");
     }
+    if (flagBool(parsed.flags, "install-mcp-tools") && flagBool(parsed.flags, "no-install-mcp-tools")) {
+        throw new Error("cannot use --install-mcp-tools and --no-install-mcp-tools together");
+    }
     if (parsed.positionals.length > 1) {
         throw new Error(`unexpected argument: ${parsed.positionals[1]}`);
     }
@@ -60,7 +71,9 @@ async function createMain(argv) {
     const installSkillsLock = flagBool(parsed.flags, "install-skills") || flagBool(parsed.flags, "no-install-skills")
         ? defaults.installSkills
         : undefined;
-    const installMcpToolsLock = flagBool(parsed.flags, "install-mcp-tools") ? true : undefined;
+    const installMcpToolsLock = flagBool(parsed.flags, "install-mcp-tools") || flagBool(parsed.flags, "no-install-mcp-tools")
+        ? defaults.installMcpTools
+        : undefined;
     const answers = interactive
         ? await askInteractiveCreateOptions(defaults, {
             installSkills: installSkillsLock,
@@ -100,6 +113,8 @@ async function lifecycleMain(argv) {
     }
     if (command === "doctor")
         return doctorCommand(argv.slice(1));
+    if (command === "setup")
+        return setupCommand(argv.slice(1));
     if (command === "rename")
         return renameCommand(argv.slice(1));
     if (command === "agents")
@@ -125,6 +140,41 @@ async function doctorCommand(argv) {
         console.log(`OK: ${root}`);
     return result.ok ? 0 : 1;
 }
+async function setupCommand(argv) {
+    const parsed = parseFlags(argv, ROOT_FLAGS);
+    if (flagBool(parsed.flags, "help")) {
+        printSetupHelp();
+        return 0;
+    }
+    assertNoArguments(parsed.positionals, "setup");
+    const root = resolve(flagString(parsed.flags, "root") ?? ".");
+    const project = await doctorProject(root);
+    const state = await readCapabilities(root);
+    const skills = await listInstalledSkills(root);
+    const skillIds = new Set(skills.map((skill) => skill.name));
+    console.log("Project Setup");
+    console.log(`root\t${root}`);
+    console.log(`doctor\t${project.ok ? "ok" : "error"}`);
+    console.log(`agent\t${state.agent}`);
+    console.log(`preset\t${state.preset}`);
+    console.log(`scope\t${state.scope}`);
+    console.log(`installed_skill_ids\t${skillIds.size}`);
+    console.log(`installed_skill_copies\t${skills.length}`);
+    console.log(`mcp_enabled\t${state.mcp_servers.length > 0 ? state.mcp_servers.join(",") : "none"}`);
+    if (!project.ok) {
+        for (const error of project.errors)
+            console.error(`ERROR: ${error}`);
+    }
+    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 smoke");
+    console.log("academic-research doctor");
+    return project.ok ? 0 : 1;
+}
 async function renameCommand(argv) {
     const parsed = parseFlags(argv, RENAME_FLAGS);
     if (flagBool(parsed.flags, "help")) {
@@ -203,8 +253,18 @@ async function skillsCommand(argv) {
     if (subcommand === "install") {
         assertOnlyOptions(parsed.flags, "skills install", ["root", "preset", "agent"]);
         const root = resolve(flagString(parsed.flags, "root") ?? ".");
-        assertNoArguments(parsed.positionals, "skills install");
-        const preset = flagString(parsed.flags, "preset") ?? "default";
+        const explicitSkills = parsed.positionals;
+        const explicitPreset = flagString(parsed.flags, "preset");
+        if (explicitSkills.length > 0) {
+            if (explicitPreset)
+                throw new Error("skills install does not accept --preset when skill ids are provided");
+            const result = await installSkillIds(root, explicitSkills, {
+                agent: flagString(parsed.flags, "agent")
+            });
+            console.log(`Installed ${result.skills?.length ?? explicitSkills.length} skill(s) with ${result.count ?? 0} command(s).`);
+            return 0;
+        }
+        const preset = explicitPreset ?? "default";
         const result = await installSkills(root, preset, {
             agent: flagString(parsed.flags, "agent")
         });
@@ -317,6 +377,24 @@ async function mcpCommand(argv) {
         console.log(`Ran ${result.count ?? 0} MCP uninstall command(s).`);
         return 0;
     }
+    if (subcommand === "smoke") {
+        assertOnlyOptions(parsed.flags, "mcp smoke", ["root"]);
+        const root = resolve(flagString(parsed.flags, "root") ?? ".");
+        const state = await readCapabilities(root);
+        const explicitSelection = parsed.positionals.length > 0;
+        const selected = explicitSelection ? parsed.positionals : state.mcp_servers;
+        assertKnownMcpServers(selected);
+        const failed = printMcpSmokeDiagnostics(selected);
+        if (!explicitSelection) {
+            const result = await doctorMcpServers(root);
+            for (const error of result.errors)
+                console.error(`ERROR: ${error}`);
+            for (const warning of result.warnings)
+                console.warn(`WARN: ${warning}`);
+            return result.ok && !failed ? 0 : 1;
+        }
+        return failed ? 1 : 0;
+    }
     if (subcommand === "doctor") {
         assertOnlyOptions(parsed.flags, "mcp doctor", ["root"]);
         const root = resolve(flagString(parsed.flags, "root") ?? ".");
@@ -461,6 +539,7 @@ function printCreateHelp() {
         "  --install-skills          Install project-local skills without prompting.",
         "  --no-install-skills       Skip project-local skill installation.",
         "  --install-mcp-tools       Run finite external MCP install commands after creation.",
+        "  --no-install-mcp-tools    Skip finite external MCP install commands.",
         "  -h, --help               Show this help.",
         "  -v, --version            Show package version."
     ].join("\n"));
@@ -476,7 +555,7 @@ function printMissingTargetHelp() {
 }
 function printLifecycleHelp() {
     console.log([
-        "Usage: academic-research <doctor|rename|agents|skills|mcp>",
+        "Usage: academic-research <doctor|setup|rename|agents|skills|mcp>",
         "",
         "Manage a generated academic research repository after creation.",
         "",
@@ -485,6 +564,17 @@ function printLifecycleHelp() {
         "  -v, --version            Show package version."
     ].join("\n"));
 }
+function printSetupHelp() {
+    console.log([
+        "Usage: academic-research setup [options]",
+        "",
+        "Print project onboarding status and next commands without changing files.",
+        "",
+        "Options:",
+        "  --root <path>            Project root. Default: current directory.",
+        "  -h, --help               Show this help."
+    ].join("\n"));
+}
 function printAgentsHelp() {
     console.log([
         "Usage: academic-research agents <list>",
@@ -502,22 +592,26 @@ function printAgentsHelp() {
 }
 function printSkillsHelp() {
     console.log([
-        "Usage: academic-research skills <list|status|presets|install|remove|uninstall|update> [options]",
+        "Usage: academic-research skills <list|status|presets|install|remove|uninstall|update> [skill-id...] [options]",
         "",
         "Manage project-local skill installs for a generated research repository.",
         "",
+        "Examples:",
+        "  academic-research skills install --preset default",
+        "  academic-research skills install source-ingestion sota-literature-review",
+        "",
         "Options:",
         "  --root <path>            Project root for list, status, install, remove, uninstall, update.",
-        "  --preset <name>          Capability preset for install.",
+        "  --preset <name>          Capability preset for install when no skill ids are provided.",
         "  --agent <id>             Agent selector for install. Default: project capability agent.",
         "  -h, --help               Show this help."
     ].join("\n"));
 }
 function printMcpHelp() {
     console.log([
-        "Usage: academic-research mcp <list|enabled|available|commands|env|enable|disable|install|uninstall|doctor> [servers...]",
+        "Usage: academic-research mcp <list|enabled|available|commands|env|enable|disable|install|uninstall|smoke|doctor> [servers...]",
         "",
-        "Manage MCP records and finite external MCP tool installs.",
+        "Manage MCP records, readiness checks, and finite external MCP tool installs.",
         "",
         "Options:",
         "  --root <path>            Project root for project-state commands.",
@@ -525,6 +619,32 @@ function printMcpHelp() {
         "  -h, --help               Show this help."
     ].join("\n"));
 }
+function printMcpSmokeDiagnostics(servers) {
+    let failed = false;
+    console.log("id\tstatus\truntime\tcheck");
+    for (const name of servers) {
+        const server = AGENT_STACK.mcp_servers[name];
+        const missingRequired = server.required_env.filter((envName) => !process.env[envName]);
+        if (missingRequired.length > 0)
+            failed = true;
+        const runtime = server.command ? [server.command, ...server.args].join(" ") : "manual setup";
+        let status = "manual";
+        if (missingRequired.length > 0) {
+            status = `missing-required-env:${missingRequired.join(",")}`;
+        }
+        else if (server.command && commandExists(server.command)) {
+            status = "runtime-found";
+        }
+        else if (server.command) {
+            status = "runtime-missing";
+        }
+        else if (server.local_service) {
+            status = "manual-local-service";
+        }
+        console.log(`${name}\t${status}\t${runtime}\t${server.smoke_test}`);
+    }
+    return failed;
+}
 function printMcpEnvironment(servers) {
     for (const name of servers) {
         const server = AGENT_STACK.mcp_servers[name];
@@ -553,6 +673,25 @@ function printMcpEnvironment(servers) {
             console.log(`${name}\tnone\t-`);
     }
 }
+function commandExists(command) {
+    if (!command)
+        return false;
+    if (command.includes("/") || command.includes("\\"))
+        return existsSync(command);
+    const pathValue = process.env.PATH ?? "";
+    const extensions = process.platform === "win32"
+        ? (process.env.PATHEXT ?? ".EXE;.CMD;.BAT;.COM").split(";")
+        : [""];
+    for (const directory of pathValue.split(delimiter).filter(Boolean)) {
+        for (const extension of extensions) {
+            const hasExtension = extension && command.toLowerCase().endsWith(extension.toLowerCase());
+            const candidate = join(directory, hasExtension ? command : `${command}${extension}`);
+            if (existsSync(candidate))
+                return true;
+        }
+    }
+    return false;
+}
 function readPackageVersion() {
     try {
         const packageJson = JSON.parse(readFileSync(join(packageRoot, "package.json"), "utf8"));

package/dist/src/project.js

@@ -138,10 +138,17 @@ export async function doctorProject(root) {
         "docs/agent/capability-profile.md",
         "docs/agent/mcp-setup.md",
         "docs/agent/generated",
+        "scripts/README.md",
         "sources/source-ledger.csv",
         "sota/literature-matrix.csv",
         "wiki/index.md",
-        "wiki/log.md"
+        "wiki/log.md",
+        "wiki/templates/source-page.md",
+        "wiki/templates/claim-page.md",
+        "wiki/templates/experiment-page.md",
+        "wiki/templates/decision-record.md",
+        "wiki/templates/reviewer-concern.md",
+        "wiki/templates/research-question.md"
     ];
     for (const relative of required) {
         if (!(await exists(join(target, relative))))
@@ -207,7 +214,7 @@ 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 ?? "0.1.6";
+    const packageSpec = process.env.CREATE_ACADEMIC_RESEARCH_PACKAGE_SPEC ?? existingSpec ?? "0.1.8";
     data.name = slug;
     data.devDependencies = {
         ...(data.devDependencies ?? {}),

package/dist/src/stack.d.ts

@@ -2,6 +2,11 @@ export interface SkillBundle {
     description: string;
     commands: string[];
 }
+export interface SkillSource {
+    description: string;
+    source: string;
+    skills: string[];
+}
 export interface CapabilityPreset {
     description: string;
     skill_bundles: string[];
@@ -30,6 +35,7 @@ export interface AgentStack {
     version: number;
     description: string;
     skill_bundles: Record<string, SkillBundle>;
+    skill_sources: Record<string, SkillSource>;
     presets: Record<string, CapabilityPreset>;
     mcp_servers: Record<string, McpServer>;
 }

package/dist/src/stack.js

@@ -22,6 +22,76 @@ export const AGENT_STACK = {
             ]
         }
     },
+    skill_sources: {
+        academic_research: {
+            description: "Academic research skills maintained by this project.",
+            source: "VincenzoImp/academic-research-skills",
+            skills: [
+                "academic-mcp-tooling",
+                "adversarial-peer-review",
+                "artifact-open-science",
+                "citation-bibliography-tooling",
+                "citation-claim-audit",
+                "cs-methodology-evaluation",
+                "cs-venue-strategy",
+                "document-conversion",
+                "ethics-data-governance",
+                "experiment-logbook",
+                "paper-writing-review",
+                "rebuttal-revision-strategy",
+                "repo-migration",
+                "research-data-analysis",
+                "research-design-positioning",
+                "research-project-maintenance",
+                "research-project-router",
+                "research-repo-reproduction",
+                "research-ui-prototyping",
+                "skill-evaluation",
+                "sota-literature-review",
+                "source-ingestion",
+                "systematic-review-prisma"
+            ]
+        },
+        superpowers: {
+            description: "General agent engineering skills from Superpowers.",
+            source: "obra/superpowers",
+            skills: [
+                "brainstorming",
+                "dispatching-parallel-agents",
+                "executing-plans",
+                "finishing-a-development-branch",
+                "receiving-code-review",
+                "requesting-code-review",
+                "subagent-driven-development",
+                "systematic-debugging",
+                "test-driven-development",
+                "using-git-worktrees",
+                "using-superpowers",
+                "verification-before-completion",
+                "writing-plans",
+                "writing-skills"
+            ]
+        },
+        anthropics: {
+            description: "Document, frontend, testing, MCP, and skill-authoring helpers.",
+            source: "anthropics/skills",
+            skills: [
+                "docx",
+                "frontend-design",
+                "mcp-builder",
+                "pdf",
+                "pptx",
+                "skill-creator",
+                "webapp-testing",
+                "xlsx"
+            ]
+        },
+        docling: {
+            description: "Document conversion helper from the Beagle collection.",
+            source: "existential-birds/beagle",
+            skills: ["docling"]
+        }
+    },
     presets: {
         minimal: {
             description: "Academic research skills only, no MCP records.",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "create-academic-research",
-  "version": "0.1.6",
+  "version": "0.1.8",
   "description": "Create and manage agent-ready academic research repositories.",
   "type": "module",
   "license": "MIT",

package/template/AGENTS.md

@@ -6,7 +6,8 @@ scholarly record.
 ## Core Rules
 
 - Preserve source originals under `sources/`, `data/raw/`, and `data/external/`.
-- Keep reusable logic in `src/`; keep notebooks for exploration and narrative output.
+- Keep reusable logic in `src/`; keep `scripts/` as thin repeatable entrypoints.
+- Keep notebooks for exploration and narrative output.
 - Tie claims to sources, datasets, experiment records, or decision records.
 - Update durable records when project knowledge changes.
 - Keep large data, generated caches, credentials, and private review material out of git.
@@ -35,6 +36,8 @@ scholarly record.
 - `wiki/synthesis.md` changes only when the project-level interpretation changes.
 - `wiki/open_questions.md` tracks unresolved questions.
 - `wiki/contradictions.md` tracks conflicts across sources, data, or runs.
+- `wiki/templates/` contains reusable source, claim, experiment, decision,
+  reviewer-concern, and research-question page structures.
 
 ## Evidence
 
@@ -45,3 +48,4 @@ scholarly record.
 - Citation issues go in `sources/bib/citation-audit.csv`.
 - SOTA records go in `sota/`.
 - Curated experiment records go in `experiments/`.
+- Repeatable command entrypoints go in `scripts/`.

package/template/README.md

@@ -41,6 +41,7 @@ npx academic-research doctor
 - `docs/agent/`: active agent workflows, capability profile, and MCP setup.
 - `docs/methodology/`: research design, evaluation plan, and validity threats.
 - `experiments/`: curated experiment registry and run records.
+- `scripts/`: thin repeatable entrypoints that call reusable code in `src/`.
 - `notebooks/`: optional exploratory and narrative notebooks.
 - `outputs/`: final figures, tables, models, and paper-supporting derived assets.
 - `reports/`: proposal, paper, slides, reviews, and rebuttal material.
@@ -56,13 +57,16 @@ 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 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
 npx academic-research mcp doctor
 ```
 
@@ -74,6 +78,12 @@ enable optional servers. `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.
 
+`setup` prints the current project capability state, installed skill counts,
+enabled MCP records, and the next onboarding commands without changing files.
+`mcp smoke` performs a non-launching MCP readiness check: it reports required
+env vars, local/manual setup, and whether client runtime commands such as `uvx`
+or `npx` are available.
+
 `default` installs the companion academic research skill package and keeps the
 MCP records focused on low-friction arXiv discovery. `literature` and `full`
 add DBLP for computer science bibliography. Credentialed, local-service, or

package/template/package.json

@@ -4,15 +4,17 @@
   "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:smoke": "academic-research mcp smoke",
     "mcp:doctor": "academic-research mcp doctor"
   },
   "devDependencies": {
-    "create-academic-research": "0.1.6"
+    "create-academic-research": "0.1.8"
   }
 }

package/template/scripts/README.md

@@ -0,0 +1,10 @@
+# Scripts
+
+Use this folder for thin, repeatable command entrypoints.
+
+Scripts should orchestrate project code, not contain core scientific logic. Put
+reusable methods, models, data transforms, and analysis functions in `src/`.
+
+Each script should make its inputs, outputs, config path, and expected side
+effects clear enough to reproduce later from `docs/reproducibility/` or an
+experiment record.

package/template/tests/test_project_structure.py

@@ -8,6 +8,7 @@ def test_core_research_structure_exists() -> None:
         "configs/default.yaml",
         "configs/capabilities.yaml",
         "docs/agent/capability-profile.md",
+        "scripts/README.md",
         "notebooks/README.md",
         "outputs/figures",
         "outputs/tables",
@@ -21,5 +22,11 @@ def test_core_research_structure_exists() -> None:
         "sota/literature-matrix.csv",
         "wiki/index.md",
         "wiki/log.md",
+        "wiki/templates/source-page.md",
+        "wiki/templates/claim-page.md",
+        "wiki/templates/experiment-page.md",
+        "wiki/templates/decision-record.md",
+        "wiki/templates/reviewer-concern.md",
+        "wiki/templates/research-question.md",
     ):
         assert (root / relative).exists()

package/template/wiki/index.md

@@ -7,3 +7,12 @@ This is the content index for the LLM-maintained project wiki.
 - [[synthesis]]
 - [[open_questions]]
 - [[contradictions]]
+
+## Templates
+
+- [[templates/source-page]]
+- [[templates/claim-page]]
+- [[templates/experiment-page]]
+- [[templates/decision-record]]
+- [[templates/reviewer-concern]]
+- [[templates/research-question]]

package/template/wiki/templates/claim-page.md

@@ -0,0 +1,24 @@
+# Claim: <claim_id>
+
+## Claim
+
+<fill: atomic claim>
+
+## Status
+
+- Verdict:
+- Confidence:
+- Last checked:
+
+## Evidence
+
+| source_or_run_id | path | support_span | verdict | notes |
+|---|---|---|---|---|
+
+## Safe Wording
+
+<fill: wording that current evidence supports>
+
+## Risk
+
+<fill: what would weaken, falsify, or narrow this claim>

package/template/wiki/templates/decision-record.md

@@ -0,0 +1,26 @@
+# Decision: <decision_id>
+
+## Context
+
+<fill: situation and constraints>
+
+## Decision
+
+<fill: chosen option>
+
+## Alternatives Considered
+
+| option | reason rejected |
+|---|---|
+
+## Evidence
+
+- Sources:
+- Experiments:
+- Reviews:
+
+## Consequences
+
+- Expected benefit:
+- Risk:
+- Review date:

package/template/wiki/templates/experiment-page.md

@@ -0,0 +1,30 @@
+# Experiment: <run_id>
+
+## Question
+
+<fill: research question or hypothesis>
+
+## Run
+
+- Date:
+- Git commit:
+- Command:
+- Config:
+- Seed:
+- Dataset:
+- Metric:
+- Output path:
+
+## Result
+
+<fill: measured outcome>
+
+## Interpretation
+
+<fill: claim status, limitations, and next action>
+
+## Links
+
+- Registry row: `experiments/registry.csv`
+- Related claims:
+- Related sources:

package/template/wiki/templates/research-question.md

@@ -0,0 +1,27 @@
+# Research Question: <rq_id>
+
+## Question
+
+<fill: answerable research question>
+
+## Scope
+
+- Population/domain:
+- Evidence type:
+- Exclusions:
+
+## Contribution Link
+
+- Candidate claim:
+- Closest prior work:
+- Delta:
+- Failure condition:
+
+## Evidence Plan
+
+| evidence_needed | path_or_source | status | risk |
+|---|---|---|---|
+
+## Current Status
+
+<fill: hypothesis, active, answered, rejected, or out of scope>

package/template/wiki/templates/reviewer-concern.md

@@ -0,0 +1,25 @@
+# Reviewer Concern: <concern_id>
+
+## Concern
+
+<fill: reviewer or internal-review concern>
+
+## Classification
+
+- Source:
+- Severity:
+- Paper location:
+- Claim or issue:
+- Action: concede | clarify | add-evidence | reframe | defend | defer
+
+## Evidence
+
+<fill: source, experiment, or manuscript evidence>
+
+## Response Plan
+
+<fill: exact response and manuscript change>
+
+## Status
+
+<fill: open, addressed, deferred, rejected with rationale>

package/template/wiki/templates/source-page.md

@@ -0,0 +1,31 @@
+# Source: <source_id>
+
+## Bibliographic Record
+
+- Title:
+- Authors:
+- Year:
+- Venue:
+- Identifiers:
+- Native path:
+- Derived path:
+- Metadata path:
+
+## Summary
+
+<fill: concise source summary>
+
+## Evidence Record
+
+- Supports:
+- Contradicts:
+- Method / data / metric:
+- Limitations:
+- Project relevance:
+- Claim strength:
+- Allowed wording:
+- Forbidden stronger wording:
+
+## Follow-Up
+
+- <fill: unresolved checks>