codebase-ai 0.3.0 → 0.3.1

package/commands/setup.md

@@ -73,6 +73,120 @@ Print: `codebase manifest: generated`
 
 ---
 
+## Step 2b — Project Structure Standardisation
+
+Scaffold the standard project structure. **Never overwrite existing files or directories.**
+
+For each path, only create if it does not already exist:
+
+```bash
+# Directories
+mkdir -p docs src/core src/modules src/interfaces tests scripts
+
+# README.md — only if missing
+[ -f README.md ] || cat > README.md << 'EOF'
+# [Project Name]
+
+[What this project does — 1-2 sentences.]
+
+## Getting Started
+
+```bash
+# install dependencies
+# run the project
+```
+
+## Development
+
+```bash
+# build
+# test
+# lint
+```
+EOF
+
+# .env.example — only if missing and no .env exists
+[ -f .env.example ] || [ -f .env ] || cat > .env.example << 'EOF'
+# Required environment variables
+# Copy to .env and fill in values
+
+# APP_PORT=3000
+# DATABASE_URL=
+# SECRET_KEY=
+EOF
+
+# docs/ARCHITECTURE.md — only if missing
+[ -f docs/ARCHITECTURE.md ] || cat > docs/ARCHITECTURE.md << 'EOF'
+# Architecture
+
+## System Overview
+
+[High-level description of how the system works.]
+
+## Key Components
+
+| Component | Purpose |
+|---|---|
+| `src/core/` | Business logic |
+| `src/modules/` | Feature modules |
+| `src/interfaces/` | Contracts, APIs, types |
+
+## Data Flow
+
+[Describe the main request/data flow through the system.]
+
+## Key Design Decisions
+
+[Document architectural decisions and their rationale here.]
+EOF
+
+# docs/IMPLEMENTATION.md — only if missing
+[ -f docs/IMPLEMENTATION.md ] || cat > docs/IMPLEMENTATION.md << 'EOF'
+# Implementation Guide
+
+## Code Organisation
+
+[How the source code is structured and why.]
+
+## Patterns & Conventions
+
+[Coding patterns, naming conventions, module rules.]
+
+## Adding Features
+
+[Step-by-step guide for contributing new functionality.]
+
+## Common Tasks
+
+[Runbook for frequent development tasks.]
+EOF
+```
+
+Print a structure report:
+```
+PROJECT STRUCTURE
+══════════════════════════════════════
+docs/                [created | exists]
+  ARCHITECTURE.md    [created | exists]
+  IMPLEMENTATION.md  [created | exists]
+  PRODUCT.md         [pending — Step 6]
+src/core/            [created | exists]
+src/modules/         [created | exists]
+src/interfaces/      [created | exists]
+tests/               [created | exists]
+scripts/             [created | exists]
+README.md            [created | exists]
+.env.example         [created | exists | skipped — .env present]
+══════════════════════════════════════
+```
+
+**Rules:**
+- Never delete or overwrite anything that already exists
+- If the project has a non-standard structure (e.g. `app/` instead of `src/`), adapt the report but do not force-rename existing dirs
+- Add any newly created paths to the Step 8 commit
+
+---
+
 ## Step 3 — GitHub labels
 
 ```bash
@@ -150,7 +264,7 @@ fi
 
 ---
 
-## Step 6 — PRODUCT.md
+## Step 6 — Docs (PRODUCT.md, ARCHITECTURE.md, IMPLEMENTATION.md)
 
 Use `codebase brief` as the primary source of project intelligence:
 
@@ -160,7 +274,7 @@ npx codebase brief 2>/dev/null > /tmp/cb-brief.json || true
 
 Read the brief. If `docs/PRODUCT.md` exists and `--refresh` not passed: show diff of stale sections, ask user to confirm updates.
 
-Otherwise generate `docs/PRODUCT.md` from:
+Otherwise generate `docs/PRODUCT.md` from (note: filename is all-caps `PRODUCT.md`):
 - `project.name`, `project.description` → Summary
 - `stack.languages`, `stack.frameworks`, `commands.*` → Tech Stack (auto-filled)
 - `patterns.architecture`, `patterns.api_style` → Context
@@ -173,9 +287,9 @@ Mark genuinely unknown sections with `[INFERRED: ...]`.
 
 ---
 
-## Step 7 — CLAUDE.md
+## Step 7 — CLAUDE.md (last — reads everything set up above)
 
-Write (or update) `CLAUDE.md` for this specific project. Read `.codebase.json` and the codebase structure to produce a file that is genuinely useful to an AI starting a fresh session on this project.
+Write (or update) `CLAUDE.md` for this specific project. At this point all other setup steps are complete — read `.codebase.json`, `docs/PRODUCT.md`, `docs/ARCHITECTURE.md`, `docs/IMPLEMENTATION.md`, and the full project structure before writing, so CLAUDE.md accurately reflects the final state of the project.
 
 **If `CLAUDE.md` already exists:** read it first. Preserve any existing sections. Only update the `<!-- codebase:start -->...<!-- codebase:end -->` block and add missing sections without removing human-authored content.
 
@@ -190,7 +304,7 @@ One paragraph describing what the project does, who it's for, and its current st
 Exact commands from `.codebase.json` → `commands.*`. Include build, dev, test, lint, typecheck.
 
 ### Architecture
-How the codebase is structured — key directories, entry points, data flow. Infer from `structure`, `patterns`, and file scanning. Be specific, not generic.
+How the codebase is structured — key directories, entry points, data flow. Pull from `docs/ARCHITECTURE.md` if it was populated, otherwise infer from `structure`, `patterns`, and file scanning. Be specific, not generic.
 
 ### Key Conventions
 Language/framework conventions detected. Coding patterns observed. Things an AI must know to not break the codebase (e.g. "zero runtime dependencies", "no cross-module state", "all DB calls go through /lib/db").
@@ -229,7 +343,7 @@ npx codebase init --quiet 2>/dev/null || true
 
 ```bash
 git checkout develop 2>/dev/null || git checkout -b develop
-git add docs/PRODUCT.md CLAUDE.md .vibekit/ .gitignore 2>/dev/null || true
+git add docs/PRODUCT.md docs/ARCHITECTURE.md docs/IMPLEMENTATION.md CLAUDE.md README.md .env.example .vibekit/ .gitignore src/ tests/ scripts/ 2>/dev/null || true
 git diff --cached --quiet || git commit -m "chore: bootstrap codebase + vibekit setup
 
 Initialized by /setup"

package/dist/index.js

@@ -551,7 +551,7 @@ ${w("SEE ALSO")}
 `:""}${w("MORE HELP")}
   ${$("codebase --help")}  Show all commands
   ${tt("https://github.com/ZySec-AI/codebase/docs","Full documentation")}
-`)}var Lc={E_NO_GIT:{message:"Not a git repository",suggestion:"Initialize git first: "+$("git init")},E_NO_PACKAGE_JSON:{message:"No package.json found",suggestion:"Initialize project: "+$("npm init")+" or "+$("pnpm init")},E_GH_NOT_AUTHENTICATED:{message:"GitHub CLI not authenticated",suggestion:"Run: "+$("gh auth login")},E_MANIFEST_NOT_FOUND:{message:".codebase.json not found",suggestion:"Run: "+$("codebase init")+" to generate it"},E_INVALID_PATH:{message:"Invalid directory path",suggestion:"Use absolute path or path relative to current directory"},E_PERMISSION_DENIED:{message:"Permission denied",suggestion:"Check file permissions or run with appropriate access"}};var oi={command:"init",subcommand:"",positionals:[],path:process.cwd(),format:"text",depth:4,categories:[],incremental:!1,quiet:!1,force:!1,verbose:!1,port:7432,tools:[],dryRun:!1,since:"",sync:!1,message:"",reason:"",examples:!1,helpCommand:!1},Zt=new 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+`)}var Lc={E_NO_GIT:{message:"Not a git repository",suggestion:"Initialize git first: "+$("git init")},E_NO_PACKAGE_JSON:{message:"No package.json found",suggestion:"Initialize project: "+$("npm init")+" or "+$("pnpm init")},E_GH_NOT_AUTHENTICATED:{message:"GitHub CLI not authenticated",suggestion:"Run: "+$("gh auth login")},E_MANIFEST_NOT_FOUND:{message:".codebase.json not found",suggestion:"Run: "+$("codebase init")+" to generate it"},E_INVALID_PATH:{message:"Invalid directory path",suggestion:"Use absolute path or path relative to current directory"},E_PERMISSION_DENIED:{message:"Permission denied",suggestion:"Check file permissions or run with appropriate access"}};var oi={command:"init",subcommand:"",positionals:[],path:process.cwd(),format:"text",depth:4,categories:[],incremental:!1,quiet:!1,force:!1,verbose:!1,port:7432,tools:[],dryRun:!1,since:"",sync:!1,message:"",reason:"",examples:!1,helpCommand:!1},Zt=new 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   > `);let o=(await ki()).toLowerCase()==="y";if(console.log(o?"Updating\u2026":`Skipped.
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@@ -620,7 +620,7 @@ ${w("BACKLOG")} (${t.backlog.length})`);for(let n of t.backlog.slice(0,10))u(`
 ${w("IN PROGRESS")} (${t.in_progress.length})`);for(let n of t.in_progress.slice(0,10)){let i=n.assignee?` @${n.assignee}`:"";u(`  #${n.number} ${n.title}${i}`)}t.in_progress.length>10&&te(`  \u2026 and ${t.in_progress.length-10} more`);let s=t.needs_verify??[];if(s.length>0){u(`
 ${w("NEEDS VERIFY")} (${s.length})`);for(let n of s.slice(0,10))u(`  #${n.number} ${n.title}`);s.length>10&&te(`  \u2026 and ${s.length-10} more`)}u(`
 ${w("DONE")} (${t.done.length} recent)`);for(let n of t.done.slice(0,5))u(`  #${n.number} ${n.title}`);t.done.length>5&&te(`  \u2026 and ${t.done.length-5} more`)}function Ra(e){S("Priority Queue");for(let t of e.priorities.slice(0,15)){let s=t.labels.length?` [${t.labels.join(", ")}]`:"",n=t.assignee?` \u2192 @${t.assignee}`:"";u(`  #${t.number} ${t.title}${s}${n}`)}}function Pa(e){S("Milestones");for(let t of e.milestones){let s=Aa(t.progress.percent),n=t.due_date?` (due: ${t.due_date.split("T")[0]})`:"";u(`
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-  ${l("Name",r)}  ${l("Description",a)}  File`),u(p);for(let d of o)u(`  ${l(d.name,r)}  ${l(d.description,a)}  ${d.file}`);u("")}import{createServer as Pc}from"http";Ce();import{readFile as _c,writeFile as Rc}from"fs/promises";import{join as Qn}from"path";async function Yn(e,t,s){let n=new URL(e,"http://localhost"),i=n.pathname;if(i==="/health")return{status:200,body:{status:"ok",version:"0.3.0"}};if(i==="/codebase/query"&&t==="GET"){let o=n.searchParams.get("path");if(!o)return{status:400,body:{error:"Missing 'path' query parameter"}};let r=await zt(s);return r?{status:200,body:Ae(r,o)??null}:{status:404,body:{error:"No manifest. POST /codebase/scan first."}}}if(i==="/codebase/scan"&&t==="POST"){let o=await W(s,{quiet:!0});return await Rc(Qn(s,".codebase.json"),JSON.stringify(o,null,2),"utf-8"),{status:200,body:o}}if(i==="/codebase"&&t==="GET"){let o=await zt(s);return o?{status:200,body:o}:{status:404,body:{error:"No manifest. POST /codebase/scan first."}}}if(i.startsWith("/codebase/")&&t==="GET"){let o=i.split("/")[2],r=await zt(s);if(!r)return{status:404,body:{error:"No manifest."}};let a=r[o];return a===void 0?{status:404,body:{error:`Category '${o}' not found.`}}:{status:200,body:a}}return{status:404,body:{error:"Not found"}}}async function zt(e){try{let t=await _c(Qn(e,".codebase.json"),"utf-8");return JSON.parse(t)}catch{return null}}function Xn(e,t){let s=Pc(async(n,i)=>{if(i.setHeader("Access-Control-Allow-Origin","*"),i.setHeader("Access-Control-Allow-Methods","GET, POST, OPTIONS"),i.setHeader("Access-Control-Allow-Headers","Content-Type"),i.setHeader("Content-Type","application/json"),n.method==="OPTIONS"){i.writeHead(200),i.end();return}try{let o=await Yn(n.url||"/",n.method||"GET",e);i.writeHead(o.status),i.end(JSON.stringify(o.body,null,2))}catch{i.writeHead(500),i.end(JSON.stringify({error:"Internal server error"}))}});s.listen(t,()=>{console.log(`codebase server running on http://localhost:${t}`),console.log(`
+  ${l("Name",r)}  ${l("Description",a)}  File`),u(p);for(let d of o)u(`  ${l(d.name,r)}  ${l(d.description,a)}  ${d.file}`);u("")}import{createServer as Pc}from"http";Ce();import{readFile as _c,writeFile as Rc}from"fs/promises";import{join as Qn}from"path";async function Yn(e,t,s){let n=new URL(e,"http://localhost"),i=n.pathname;if(i==="/health")return{status:200,body:{status:"ok",version:"0.3.1"}};if(i==="/codebase/query"&&t==="GET"){let o=n.searchParams.get("path");if(!o)return{status:400,body:{error:"Missing 'path' query parameter"}};let r=await zt(s);return r?{status:200,body:Ae(r,o)??null}:{status:404,body:{error:"No manifest. POST /codebase/scan first."}}}if(i==="/codebase/scan"&&t==="POST"){let o=await W(s,{quiet:!0});return await Rc(Qn(s,".codebase.json"),JSON.stringify(o,null,2),"utf-8"),{status:200,body:o}}if(i==="/codebase"&&t==="GET"){let o=await zt(s);return o?{status:200,body:o}:{status:404,body:{error:"No manifest. POST /codebase/scan first."}}}if(i.startsWith("/codebase/")&&t==="GET"){let o=i.split("/")[2],r=await zt(s);if(!r)return{status:404,body:{error:"No manifest."}};let a=r[o];return a===void 0?{status:404,body:{error:`Category '${o}' not found.`}}:{status:200,body:a}}return{status:404,body:{error:"Not found"}}}async function zt(e){try{let t=await _c(Qn(e,".codebase.json"),"utf-8");return JSON.parse(t)}catch{return null}}function Xn(e,t){let s=Pc(async(n,i)=>{if(i.setHeader("Access-Control-Allow-Origin","*"),i.setHeader("Access-Control-Allow-Methods","GET, POST, OPTIONS"),i.setHeader("Access-Control-Allow-Headers","Content-Type"),i.setHeader("Content-Type","application/json"),n.method==="OPTIONS"){i.writeHead(200),i.end();return}try{let o=await Yn(n.url||"/",n.method||"GET",e);i.writeHead(o.status),i.end(JSON.stringify(o.body,null,2))}catch{i.writeHead(500),i.end(JSON.stringify({error:"Internal server error"}))}});s.listen(t,()=>{console.log(`codebase server running on http://localhost:${t}`),console.log(`
 Endpoints:`),console.log("  GET  /health              Health check"),console.log("  GET  /codebase            Full manifest"),console.log("  GET  /codebase/:category  Single category"),console.log("  GET  /codebase/query?path=stack.languages"),console.log("  POST /codebase/scan       Trigger re-scan")}),process.on("SIGINT",()=>{s.close(),process.exit(0)}),process.on("SIGTERM",()=>{s.close(),process.exit(0)})}var pe=es(process.argv.slice(2));ee(pe.quiet);Qt(pe.verbose);pe.helpCommand&&pe.command&&ts(pe.command);var Dc={scan:Ge,init:bn,brief:yn,next:wn,setup:Tt,query:vn,issue:En,status:Rn,mcp:Ln,doctor:qn,fix:Un,release:Bn,plan:zn,skills:Vn,serve:e=>(Xn(e.path,e.port??3e3),Promise.resolve()),"scan-only":Ge};os().catch(()=>{});var[Ac]=process.versions.node.split(".").map(Number);Ac<20&&(console.error(`Error: Node.js 20 or higher is required. You are running v${process.versions.node}.`),console.error("Upgrade: https://nodejs.org"),process.exit(1));var Zn=Dc[pe.command];Zn||(v(`Unknown command: ${pe.command}`),h(`Run ${w("codebase --help")} to see all commands.`),process.exit(1));Zn(pe).catch(e=>{v(`Error: ${e.message}`);let t=e.message.toLowerCase();t.includes("not a git repository")?h(`Initialize git first: ${w("git init")}`):t.includes("permission denied")?h("Check file permissions or run with appropriate access"):t.includes("enoent")&&t.includes("gh")?h(`GitHub CLI (gh) is not installed. Install it: ${w("brew install gh && gh auth login")}`):t.includes("no such file")?h("Check that the path is correct"):t.includes("github")&&(h(`Ensure GitHub CLI is installed: ${w("gh --version")}`),h(`Authenticate: ${w("gh auth login")}`)),process.exit(1)});
 //# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "codebase-ai",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "description": "One command. Every AI tool understands your project instantly.",
   "type": "module",
   "homepage": "https://github.com/ZySec-AI/codebase",