@polycode-projects/seonix 0.10.6 → 0.10.9

package/bin/cli.mjs

@@ -22,6 +22,10 @@
 //   seonix cli index_repository '{"multi_root":"<abs-dir>"}' → estate discovery: every immediate
 //     child directory carrying a .git (dir or file) is indexed as a repo, merged into
 //     <multi_root>/.seonix/ (discovered/skipped counts logged to stderr)
+//   seonix cli index_repository --multi-root [path]           → same, flag form — no JSON
+//     quoting needed; a bare `--multi-root` (no path) defaults to cwd, e.g. `cd <estate> &&
+//     npx seonix cli index_repository --multi-root`. `--repo-path [path]` and `--out-root
+//     <path>` (always needs a value) are the flag forms of the other two path args.
 //   seonix cli sync '{"multi_root":"<abs-dir>"}' → incrementally re-index the estate: fingerprint
 //     every child repo (git/gitparent/plain), re-extract ONLY the changed ones (per-repo cache in
 //     .seonix/cache/), one union rebuild = exact full-re-index. Unchanged-everything = byte-stable
@@ -54,7 +58,7 @@
 
 import { dirname, join } from "node:path";
 import { existsSync } from "node:fs";
-import { readFile, writeFile } from "node:fs/promises";
+import { readFile, writeFile, readdir } from "node:fs/promises";
 import { fileURLToPath } from "node:url";
 import { startServer } from "../src/server.mjs";
 import { dispatchTool, buildContextBundle, TOOLS } from "../src/server.mjs";
@@ -80,6 +84,32 @@ function parsePayload(payload) {
   catch { return null; }
 }
 
+const INDEX_FLAG_KEYS = { "--multi-root": "multi_root", "--repo-path": "repo_path", "--out-root": "out_root" };
+
+/** Flag-style alternative to index_repository's JSON payload — `--multi-root [path]` /
+ *  `--repo-path [path]` (also `--flag=path`), so `npx seonix cli index_repository
+ *  --multi-root` works without JSON-quoting a path. A bare `--multi-root`/`--repo-path`
+ *  (no path following, or the payload ends there) defaults to cwd, matching the JSON form's
+ *  own cwd-default convention. `--out-root` always needs an explicit value — there's no
+ *  sensible cwd default for it. Returns an args object shaped like the JSON payload, or
+ *  null if the first token isn't a recognised flag (falls back to JSON parsing). */
+function parseIndexFlags(argv) {
+  const args = {};
+  for (let i = 0; i < argv.length; i++) {
+    const tok = argv[i];
+    const eq = tok.indexOf("=");
+    const flag = eq === -1 ? tok : tok.slice(0, eq);
+    const key = INDEX_FLAG_KEYS[flag];
+    if (!key) return null;
+    if (eq !== -1) { args[key] = tok.slice(eq + 1); continue; }
+    const next = argv[i + 1];
+    if (next !== undefined && !next.startsWith("--")) { args[key] = next; i++; }
+    else if (key === "multi_root" || key === "repo_path") { args[key] = process.cwd(); }
+    else return null;
+  }
+  return Object.keys(args).length ? args : null;
+}
+
 /** Nearest ancestor of `startDir` (itself first) containing a .seonix/ directory, or null. */
 function findIndexRoot(startDir = process.cwd()) {
   let dir = startDir;
@@ -113,6 +143,36 @@ function defaultRepoPath(args, { mustExist = true } = {}) {
   return args;
 }
 
+/** Single-mode index_repository against a directory that (a) isn't itself a git repo and
+ *  (b) has ≥2 immediate child directories that ARE — the exact signature of an estate root
+ *  mistaken for one flat repo (the `multi_root` docs' own warning: "repo_path would index it
+ *  as one flat repo"). Silent consequence: git history extraction fails against the non-repo
+ *  root (0 commits, no error the caller necessarily notices among the rest of the index
+ *  output), module ids aren't per-repo-prefixed, and every sub-repo gets flattened together.
+ *  Best-effort (readdir failure just means no warning, never a crash) — this only ADDS a
+ *  warning in a case that previously silently mis-indexed, so it can't change any existing
+ *  single-repo index's output. */
+async function warnIfLooksLikeEstateRoot(repoPath) {
+  if (existsSync(join(repoPath, ".git"))) return;
+  let entries;
+  try { entries = await readdir(repoPath, { withFileTypes: true }); }
+  catch { return; }
+  let childRepoCount = 0;
+  for (const e of entries) {
+    if (e.isDirectory() && existsSync(join(repoPath, e.name, ".git"))) childRepoCount++;
+    if (childRepoCount >= 2) break;
+  }
+  if (childRepoCount >= 2) {
+    process.stderr.write(
+      `seonix: WARNING — ${repoPath} has no .git of its own, but multiple child directories do. ` +
+        "This looks like a multi-repo estate root, not a single repo — indexing it this way flattens " +
+        "every sub-repo together with NO git history (git log fails against a non-repo root) and no " +
+        "per-repo module-id prefixing. If that's not what you want, re-run with " +
+        `'{"multi_root":"${repoPath}"}' instead, which discovers each child repo and indexes it properly.\n`,
+    );
+  }
+}
+
 // Hot tools (server.mjs's TOOLS) carry an inputSchema but no example value, so their
 // example-args + primary-arg-key aren't derivable the way COLD_TOOLS' are — hand-maintained
 // here, right next to COLD_TOOLS' import, so a new hot tool is a one-line addition in both places.
@@ -482,9 +542,13 @@ async function main() {
     // '{"repo_paths":[…],"out_root":"<abs>"}' (explicit n-repo merge) or
     // '{"multi_root":"<abs>"}' (discover child repos, merge into <multi_root>/.seonix/).
     if (sub === "index_repository") {
-      const args = parsePayload(payload);
+      const isFlagForm = payload !== undefined && payload.startsWith("--");
+      const args = isFlagForm ? parseIndexFlags(process.argv.slice(4)) : parsePayload(payload);
       if (args === null) {
-        process.stderr.write("seonix: index_repository expects a JSON arg, e.g. '{\"repo_path\":\"/abs\"}'\n");
+        process.stderr.write(
+          "seonix: index_repository expects a JSON arg, e.g. '{\"repo_path\":\"/abs\"}', " +
+            "or a flag: --multi-root [path], --repo-path [path], --out-root <path>\n",
+        );
         process.exit(2);
       }
       const given = ["repo_path", "repo_paths", "multi_root"].filter((k) => args[k] !== undefined);
@@ -557,6 +621,7 @@ async function main() {
       };
 
       if (args.repo_path) {
+        await warnIfLooksLikeEstateRoot(args.repo_path);
         const { graphFile, counts, summary } = await indexRepository(args.repo_path, { ignores: args.ignores !== false, historyDepth, extraIgnores, languages: tomlLanguages, interfaces: tomlInterfaces });
         emitSummary(graphFile, counts, "");
         // A1: the human summary MD goes to STDOUT (bench ignores index stdout — safe;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@polycode-projects/seonix",
-  "version": "0.10.6",
+  "version": "0.10.9",
   "private": false,
   "type": "module",
   "description": "SEONIX — a deterministic, offline, $0 code-graph tool that makes a cheap coding agent edit like an expensive one. Indexes a repo with Python ast + git (zero model calls) and renders a bounded edit-digest.",
@@ -87,7 +87,7 @@
   },
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.29.0",
-    "@polycode-projects/the-mechanical-code-talker": "^0.9.4",
+    "@polycode-projects/the-mechanical-code-talker": "^0.9.8",
     "cytoscape": "^3.30.0",
     "smol-toml": "^1.7.0",
     "tree-sitter": "^0.21.1",