@polycode-projects/seonix 0.9.0 → 0.10.0

package/README.md

@@ -46,13 +46,13 @@ network calls, **$0**.
 
 ```bash
 # 1. index your repo (deterministic, offline) — writes a machine-local .seonix/
-seonix cli index_repository '{"repo_path":"/abs/path/to/repo"}'
+cd /path/to/repo && seonix cli index_repository
 
 # 2. self-locate the touched modules from the task text (no human-chosen target)
-seonix cli seonix_search '{"repo_path":"/abs/path/to/repo","query":"<your task>"}'
+seonix cli seonix_search '{"query":"<your task>"}'
 
 # 3. render the bounded edit digest for those modules
-seonix cli digest '{"repo_path":"/abs/path/to/repo","modules":["<top hits>"]}' > digest.txt
+seonix cli digest '{"modules":["<top hits>"]}' > digest.txt
 
 # 4. inject digest.txt once at session start, then run your coding agent
 claude --prompt "Use the seonix digest below to localise and make the change. $(cat digest.txt)"
@@ -60,6 +60,13 @@ claude --prompt "Use the seonix digest below to localise and make the change. $(
 
 Add `.seonix/` to your `.gitignore`; it is machine-local and rebuilt from source.
 
+The JSON argument is optional on every `cli` command: an omitted `repo_path`
+resolves to the nearest ancestor of the current directory (current directory
+first) containing a `.seonix/`, so query commands work from any subdirectory of
+an indexed repo. `index_repository` falls back to the current directory when
+nothing is indexed yet; query commands print a one-line error instead. An
+explicit `repo_path` always wins.
+
 ## Indexing multiple repositories
 
 `index_repository` takes one of three argument forms:
@@ -117,14 +124,17 @@ should start it with cwd = the indexed worktree.
 ### `cli index_repository` — build the graph
 
 ```bash
+seonix cli index_repository                       # no arg: index the repo you are in
 seonix cli index_repository '{"repo_path":"/abs/repo"}'
 seonix cli index_repository '{"repo_paths":["/abs/repo1","/abs/repo2"],"out_root":"/abs/dir"}'
 seonix cli index_repository '{"multi_root":"/abs/estate"}'
 ```
 
 `repo_path` / `repo_paths`+`out_root` / `multi_root` are mutually exclusive — pass
-exactly one (or let `seonix.toml`'s `repositories` supply the set when none is
-given explicitly). Shared JSON options:
+at most one. When none is given, `seonix.toml`'s `repositories` supplies the set
+if present; otherwise the target defaults to the nearest ancestor of the current
+directory carrying a `.seonix/` (re-index), else the current directory itself
+(first index). Shared JSON options:
 
 - `ignores` (bool, default `true`) — honour the repo's `.seonixignore`. Pass
   `"ignores":false` to index everything regardless (the bench harness always
@@ -235,7 +245,9 @@ seonix cli seonix_context '{"symbol":"buildContextBundle","repo_path":"/abs/repo
 Any sub-command name that isn't one of the above routes straight to the MCP tool
 dispatcher, so any tool in the server's surface — cold or hot — is invokable from
 Bash with no MCP connection. `repo_path` in the JSON arg selects the target
-graph; every other key is passed through as the tool's own arguments.
+graph; omitted, it defaults to the nearest ancestor of the current directory
+containing a `.seonix/` (a clean one-line error when there is none). Every other
+key is passed through as the tool's own arguments.
 
 ### `hook-augment` — PreToolUse Grep/Glob augmenter
 
@@ -316,7 +328,11 @@ seonix supplies the graph through tmct's provider seam.
 Two opt-in/opt-out environment knobs, orthogonal to everything above:
 `SEONIX_STORE=sqlite` turns on the resident `node:sqlite` store as a derived,
 rebuildable companion to `graph.json` (rebuild it explicitly with `cli
-store_rebuild`; unset, nothing sqlite loads). `SEONIX_GRAPH_FORMAT` controls the
+store_rebuild`; unset, nothing sqlite loads). The variable must be **exported**
+(`export SEONIX_STORE=sqlite`) — a plain shell assignment is invisible to the
+`seonix` child process, and the JSON path runs instead. The index summary's
+`store:` line states which mode actually ran (`store: sqlite (graph.db +
+graph.json)` only when `graph.db` was built). `SEONIX_GRAPH_FORMAT` controls the
 graph's on-disk wire format — the interned v2 form is the shipped default;
 set `SEONIX_GRAPH_FORMAT=1` to opt back out to the legacy v1 form.
 
@@ -325,7 +341,7 @@ set `SEONIX_GRAPH_FORMAT=1` to opt back out to the legacy v1 form.
 An optional `seonix.toml` at a repo (or estate) root steers indexing and
 scoring. Absent file = shipped defaults, byte-for-byte today's behaviour.
 `seonix init` (or `seonix init --dotnet` for an estate) seeds a commented
-template — see `packages/seonix/templates/seonix.toml` and
+template — see `templates/seonix.toml` and
 `templates/seonix-dotnet.toml` for the full annotated reference.
 
 - **`repositories`** — the repo set for an estate config: an inline array of

package/bin/cli.mjs

@@ -6,6 +6,12 @@
 //   seonix cli index_repository '{"repo_path":"<abs>"}' → deterministic index
 //     (honours <repo>/.seonixignore — gitignore-subset patterns; pass
 //      `"ignores":false` in the JSON arg to index everything regardless)
+//     The JSON arg is OPTIONAL for every `cli` command: an omitted repo_path defaults
+//     to the nearest ancestor of cwd (cwd first) containing a .seonix/ directory —
+//     so a bare `seonix cli index_repository` indexes the repo you are in, and query
+//     commands run from any subdirectory of an indexed repo. index_repository falls
+//     back to cwd when nothing is indexed yet (it creates the index); query commands
+//     error cleanly instead. An explicit repo_path always wins, unchanged.
 //   seonix cli index_repository '{"repo_paths":["<abs1>","<abs2>",…],"out_root":"<abs-dir>"}' → index
 //     n repos into ONE merged graph at <out_root>/.seonix/ (module ids prefixed with each repo's
 //     directory basename; out_root defaults to the paths' deepest common ancestor directory).
@@ -39,7 +45,7 @@
 // graph artifact to <repo_path>/.seonix/graph.json; the server (started with
 // cwd = that repo) loads it by default. No flags, no config files.
 
-import { join } from "node:path";
+import { dirname, join } from "node:path";
 import { existsSync } from "node:fs";
 import { readFile, writeFile } from "node:fs/promises";
 import { fileURLToPath } from "node:url";
@@ -52,7 +58,7 @@ import * as source from "../src/source.mjs";
 import { parseEntities, renderSearch, rankModulesByProximity, searchModulesRanked, selectRankedModules, DEFAULT_SCORE_GAP } from "../src/codegraph.mjs";
 import { loadTomlConfig, normalizeConfig, mergeEffective, CONFIG_FILE } from "../src/toml-config.mjs";
 import { compileGlobs } from "../src/walk.mjs";
-import { createTelemetry } from "../src/telemetry.mjs";
+import { createTelemetry, truncateStr, looksLikeMiss } from "../src/telemetry.mjs";
 
 /** Build a config pointed at a specific repo's artifact (for `cli` sub-commands that
  *  take a repo_path), or fall back to the cwd-derived default. */
@@ -67,6 +73,39 @@ function parsePayload(payload) {
   catch { return null; }
 }
 
+/** Nearest ancestor of `startDir` (itself first) containing a .seonix/ directory, or null. */
+function findIndexRoot(startDir = process.cwd()) {
+  let dir = startDir;
+  for (;;) {
+    if (existsSync(join(dir, ".seonix"))) return dir;
+    const parent = dirname(dir);
+    if (parent === dir) return null;
+    dir = parent;
+  }
+}
+
+/** Default an omitted repo_path for a `cli` command. Precedence:
+ *    1. explicit repo_path — always wins, args returned untouched (byte-identical to today);
+ *    2. SEONIX_GRAPH_FILE — also untouched (configFor's loadConfig fallback consumes it);
+ *    3. the nearest ancestor of cwd (cwd first) carrying a .seonix/ → written into args.repo_path;
+ *    4. nothing found: commands that READ an index (`mustExist`) get a one-line error + exit 2;
+ *       index_repository falls back to cwd (it CREATES the index there).
+ *  Mutating args means downstream configFor/tomlFor/telemetry all see the resolved repo. */
+function defaultRepoPath(args, { mustExist = true } = {}) {
+  if (args.repo_path !== undefined) return args;
+  // The env override only steers commands that READ a graph (query commands); index_repository
+  // writes to <repo>/.seonix and never consumes SEONIX_GRAPH_FILE, so it still defaults.
+  if (mustExist && process.env.SEONIX_GRAPH_FILE && process.env.SEONIX_GRAPH_FILE.trim()) return args;
+  const root = findIndexRoot();
+  if (root) { args.repo_path = root; return args; }
+  if (mustExist) {
+    process.stderr.write("seonix: no .seonix index found here or above — run `seonix cli index_repository` first or pass repo_path\n");
+    process.exit(2);
+  }
+  args.repo_path = process.cwd();
+  return args;
+}
+
 /** Load a repo's seonix.toml as a normalized config, or null. Returns null IMMEDIATELY when
  *  `args.config === false` (the BENCH-IMMUNITY flag — an arm's index/locate/digest must NEVER read a
  *  subject repo's seonix.toml) OR when no seonix.toml exists. So on the bench path, and with no
@@ -163,6 +202,7 @@ async function runDigest(args) {
   // stdout is the digest injected into the no-MCP arm, so telemetry must never touch it. The
   // seonix.toml [telemetry] toggle rides in via `toml`; SEONIX_TELEMETRY still wins both ways.
   const tel = createTelemetry({ env: process.env, config: configFor(repoPath), toml, surface: "cli" });
+  const t0 = Date.now();
   const tune = resolveDigestTune(args, toml);
   let modules = Array.isArray(args.modules) ? args.modules.slice(0, DIGEST_MODULE_CAP) : [];
   let autoSelected = null; // for the header, when `query` drove selection
@@ -236,10 +276,14 @@ async function runDigest(args) {
   process.stdout.write(out);
   // One telemetry line for the digest surface: the selected modules + the effective tier/topup the
   // header already carries, plus the injected body size. `tier` here MUST equal the header's tier=.
+  // (wh dogfood backlog #6): duration + a miss flag — a query-mode digest that selected zero
+  // modules is an unambiguous miss (autoSelected is only set in query mode).
   tel?.record({
     surface: "digest",
-    query: args.query ? { raw: args.query } : undefined,
+    query: args.query ? { raw: truncateStr(args.query) } : undefined,
     response: { count: emitted, node_ids: modules, tier: effTier, topup },
+    perf: { ms_total: Date.now() - t0 },
+    quality: { miss: autoSelected ? autoSelected.length === 0 : emitted === 0 },
     cost: { returned_chars: out.length, returned_tokens_est: Math.ceil(out.length / 4) },
   });
 }
@@ -320,15 +364,21 @@ async function main() {
       }
       // seonix.toml: config dir = the explicit repo/estate path, else out_root, else cwd (where the
       // file sits). Skipped entirely on the bench path (config:false → tomlFor null → byte-identical).
-      const toml = await tomlFor(args.repo_path || args.multi_root || args.out_root || process.cwd(), args);
+      let toml = await tomlFor(args.repo_path || args.multi_root || args.out_root || process.cwd(), args);
       warnUnwired(toml);
       // repositories: seonix.toml MAY supply the repo set when NO explicit path arg is given
       // (explicit repo_path/repo_paths/multi_root always win).
       const tomlRepos = (given.length === 0 && toml && Array.isArray(toml.repositories) && toml.repositories.length)
         ? toml.repositories : null;
       if (given.length === 0 && !tomlRepos) {
-        process.stderr.write("seonix: index_repository requires repo_path, repo_paths or multi_root\n");
-        process.exit(2);
+        // No path arg and no seonix.toml repo set: default to the nearest ancestor of cwd
+        // carrying a .seonix/ (re-index it), else cwd itself (first index — it creates .seonix/).
+        defaultRepoPath(args, { mustExist: false });
+        // The resolved root may carry its own seonix.toml (cwd can be a subdirectory) — re-read there.
+        if (args.repo_path && args.repo_path !== process.cwd()) {
+          toml = await tomlFor(args.repo_path, args);
+          warnUnwired(toml);
+        }
       }
       // A5 `history_depth`: unified cap over BOTH git-history passes. 0 = skip history entirely;
       // N>0 = `git log -n N`; absent = today's defaults. Precedence: explicit arg > seonix.toml
@@ -449,7 +499,7 @@ async function main() {
         process.stderr.write("seonix: digest expects a JSON arg, e.g. '{\"repo_path\":\"/abs\",\"modules\":[…]}'\n");
         process.exit(2);
       }
-      await runDigest(args);
+      await runDigest(defaultRepoPath(args));
       return;
     }
 
@@ -463,6 +513,24 @@ async function main() {
         process.stderr.write("seonix: seonix_locate expects a JSON arg, e.g. '{\"query\":\"…\",\"repo_path\":\"/abs\"}'\n");
         process.exit(2);
       }
+      // Tool honesty (wh dogfood T7): seonix_locate used to print NOTHING and exit 0 for
+      // any input without a query ({}, {"symbol":…}, {"bogus":1}) — an empty ranking is
+      // indistinguishable from success in a tool loop. Bad/missing args are now a one-line
+      // error naming the valid keys + a nonzero exit, like the generic dispatchTool route.
+      const LOCATE_KEYS = [
+        "query", "raw_query", "repo_path", "config", "limit", "spiral", "spiral_depth",
+        "demote_nonprod", "call_adjacency", "impl_of_interface", "beam_search", "beam_width", "literal_mention",
+      ];
+      const unknownKeys = Object.keys(args).filter((k) => !LOCATE_KEYS.includes(k));
+      if (unknownKeys.length) {
+        process.stderr.write(`seonix: unknown argument(s) for seonix_locate: ${unknownKeys.join(", ")}. Valid: ${LOCATE_KEYS.join(", ")}.\n`);
+        process.exit(2);
+      }
+      if (!String(args.query || "").trim()) {
+        process.stderr.write("seonix: seonix_locate requires a non-empty \"query\" (free text to rank modules against). For a single symbol use seonix_search or seonix_describe.\n");
+        process.exit(2);
+      }
+      defaultRepoPath(args);
       const config = configFor(args.repo_path);
       // seonix.toml [tune] defaults the locate levers (arg > seonix.toml > default). Skipped on the
       // bench path (config:false → tomlFor null) and when no seonix.toml exists → byte-identical.
@@ -471,6 +539,7 @@ async function main() {
       // Opt-in telemetry (default OFF → null → no-op, no file). stdout is the ranked list the rig
       // parses, so telemetry is LOG FILE ONLY. seonix.toml [telemetry] rides in via `toml`.
       const tel = createTelemetry({ env: process.env, config, toml, surface: "cli" });
+      const t0 = Date.now();
       const tune = resolveLocateTune(args, toml);
       try {
         const graph = parseEntities(await source.fetchEntities(config));
@@ -510,15 +579,18 @@ async function main() {
             : {}),
         });
         process.stdout.write(ranked.map((r) => `${r.path}\t${r.score}`).join("\n") + "\n");
-        // Telemetry for the locate surface: the ranked count + the top few paths/scores.
+        // Telemetry for the locate surface: the ranked count + the top few paths/scores, plus
+        // (wh dogfood backlog #6) duration + a miss flag (an empty ranking is an unambiguous miss).
         tel?.record({
           surface: "locate",
-          query: { raw: String(args.query || "") },
+          query: { raw: truncateStr(String(args.query || "")) },
           response: {
             count: ranked.length,
             node_ids: ranked.slice(0, 3).map((r) => r.path),
             scores: ranked.slice(0, 3).map((r) => r.score),
           },
+          perf: { ms_total: Date.now() - t0 },
+          quality: { miss: ranked.length === 0 },
         });
       } catch (e) {
         process.stderr.write(`seonix: ${e?.message || e}\n`);
@@ -539,6 +611,7 @@ async function main() {
         process.stderr.write("seonix: browser_link expects a JSON arg, e.g. '{\"query\":\"classes that change with render\"}'\n");
         process.exit(2);
       }
+      defaultRepoPath(args);
       const config = configFor(args.repo_path);
       const { buildTemporalGraph, gitCommitOrder } = await import("../src/browser.mjs");
       const { nlToQuery, validateLink, encodeViewState, VIEW_DEFAULTS } = await import("../src/temporal.mjs");
@@ -578,6 +651,7 @@ async function main() {
         process.stderr.write("seonix: store_rebuild expects a JSON arg, e.g. '{\"repo_path\":\"/abs\"}'\n");
         process.exit(2);
       }
+      defaultRepoPath(args);
       const { graphFile } = configFor(args.repo_path);
       const { readFile, stat } = await import("node:fs/promises");
       const { writeStore, storeFileFor, verifyStore } = await import("../src/store.mjs");
@@ -612,17 +686,23 @@ async function main() {
         process.stderr.write(`seonix: ${sub} expects a JSON arg, e.g. '{"symbol":"<name>"}'\n`);
         process.exit(2);
       }
+      defaultRepoPath(args);
       const config = configFor(args.repo_path);
       // seonix.toml [telemetry] toggle for the generic tool surface (byte-identical with no toml:
       // tomlFor short-circuits to null on the bench path and when no seonix.toml exists).
       const toml = await tomlFor(args.repo_path, args);
       const tel = createTelemetry({ env: process.env, config, toml, surface: "cli" });
+      const t0 = Date.now();
       try {
         const text = await dispatchTool(sub, args, { config });
         process.stdout.write(text + "\n");
-        // Telemetry for the generic tool surface: which tool + how many chars it returned.
+        // Telemetry for the generic tool surface: which tool + how many chars it returned, plus
+        // (wh dogfood backlog #6) the args text/duration/hit-miss the log previously omitted.
         tel?.record({
           tool: sub,
+          query: { raw: truncateStr(JSON.stringify(args)) },
+          perf: { ms_total: Date.now() - t0 },
+          quality: { miss: looksLikeMiss(text) },
           cost: { returned_chars: text.length, returned_tokens_est: Math.ceil(text.length / 4) },
         });
       } catch (e) {
@@ -632,7 +712,8 @@ async function main() {
       return;
     }
 
-    process.stderr.write("seonix: `cli` needs a sub-command (index_repository | digest | <toolName>)\n");
+    process.stderr.write("seonix: `cli` needs a sub-command (index_repository | digest | <toolName>). " +
+      "The JSON arg is optional — an omitted repo_path defaults to the nearest ancestor of cwd with a .seonix/ index.\n");
     process.exit(2);
   }
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@polycode-projects/seonix",
-  "version": "0.9.0",
+  "version": "0.10.0",
   "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.",
@@ -9,8 +9,7 @@
   "homepage": "https://seonix.polycode.co.uk",
   "repository": {
     "type": "git",
-    "url": "git+https://gitlab.com/polycode-projects/seonix.git",
-    "directory": "packages/seonix"
+    "url": "git+https://gitlab.com/polycode-projects/seonix.git"
   },
   "bugs": {
     "url": "https://gitlab.com/polycode-projects/seonix/-/issues"
@@ -42,9 +41,51 @@
   "publishConfig": {
     "access": "public"
   },
+  "workspaces": [
+    "infra"
+  ],
+  "scripts": {
+    "setup": "node scripts/setup.mjs",
+    "bench": "node bench/run.mjs",
+    "bench:quick": "node bench/run.mjs --instances 1 --runs 1",
+    "join:telemetry": "node scripts/join-telemetry.mjs",
+    "bench:lite": "node bench/run.mjs --suite lite",
+    "bench:seonix": "node bench/run.mjs --suite django-lh --arms seonix,seonix-min --runs 5",
+    "bench:baseline": "node scripts/use-baseline.mjs",
+    "proof": "node scripts/proof-demo.mjs",
+    "smoke": "node bench/smoke.mjs --suite django-lh",
+    "report": "node bench/report.mjs",
+    "all": "npm run setup && npm run bench && npm run report",
+    "clean": "node scripts/clean.mjs",
+    "verify:counts": "node scripts/verify-counts.mjs",
+    "verify:sanity": "node scripts/verify-sanity.mjs",
+    "verify:index": "node scripts/verify-index.mjs",
+    "verify:query": "node scripts/verify-query.mjs",
+    "verify:review": "node scripts/verify-review.mjs",
+    "verify:loop": "node scripts/verify-loop.mjs",
+    "refs": "node scripts/fetch-references.mjs",
+    "refs:embeddings": "node scripts/fetch-embeddings.mjs",
+    "audit": "npm audit --audit-level=high",
+    "audit:fix": "npm audit fix",
+    "test:root": "node --test \"test/**/*.test.mjs\"",
+    "test": "npm run test:root && npm run chrono:test",
+    "chrono:build": "node chronograph/build.mjs",
+    "chrono:serve": "node chronograph/serve.mjs",
+    "chrono:test": "node --test \"chronograph/test/**/*.test.mjs\"",
+    "test:all": "npm run test",
+    "seonix": "node bin/cli.mjs",
+    "seonix:viz": "node bin/cli.mjs viz --",
+    "e2e:install": "npx playwright install chromium --with-deps",
+    "e2e": "playwright test",
+    "e2e:site": "playwright test site.behaviour.test.js",
+    "e2e:prod": "SEONIX_E2E_BASE_URL=https://seonix.polycode.co.uk playwright test site.behaviour.test.js",
+    "site:prompts": "node scripts/site-prompts.mjs",
+    "build:ask-bundle": "node scripts/build-ask-bundle.mjs",
+    "site:gen": "npm run build:ask-bundle && node bin/cli.mjs viz --focus buildContextBundle --depth 2 --repo-url https://gitlab.com/polycode-projects/seonix --site-nav --out site/seonix-graph.html --data-out site/seonix-graph-data.json --browser-out site/code-browser.html --browser-data-out site/code-browser-data.json --timeline-out site/timeline.html && npm run site:prompts"
+  },
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.29.0",
-    "@polycode-projects/the-mechanical-code-talker": "^0.8.0",
+    "@polycode-projects/the-mechanical-code-talker": "^0.8.2",
     "cytoscape": "^3.30.0",
     "smol-toml": "^1.7.0",
     "tree-sitter": "^0.21.1",
@@ -52,8 +93,8 @@
     "tree-sitter-java": "^0.21.0",
     "typescript": "~5.6.2"
   },
-  "scripts": {
-    "test": "node --test \"test/**/*.test.mjs\"",
-    "viz": "node bin/cli.mjs viz"
+  "devDependencies": {
+    "@playwright/test": "^1.56.0",
+    "esbuild": "^0.28.1"
   }
 }