agent-doc-system 1.1.0 → 1.2.0

package/adapters/typescript.mjs

@@ -44,7 +44,7 @@ export class TypeScriptAdapter extends Adapter {
     const routes = [];
     for (const base of ["src/app", "app", "src/pages", "pages"]) {
       if (!repo.isDir(unit.root + "/" + base)) continue;
-      for (const f of repo.walk(unit.root + "/" + base)) {
+      for (const f of repo.walkUnit(unit.root, unit.root + "/" + base)) {
         const routePath = routeFor(unit.root, base, f);
         if (!routePath) continue;
         const rpr = prov.add("observed", f, "route-extractor", ["der:" + compRef + ":/routes"]);

package/bin/agentdoc.mjs

@@ -275,9 +275,9 @@ try {
       }
     }
     const ctx = queryContext(graph, needle, { budget });
-    if (opt("md")) out(renderContext(ctx));
+    if (opt("md")) out(renderContext(ctx, { budget }));
     else if (opt("json")) out(ctx, true);
-    else out(renderContext(ctx));
+    else out(renderContext(ctx, { budget }));
   } else if (cmd === "impact") {
     // Impact answers a question about the working tree, so it compiles in
     // memory rather than reading the committed graph. Refusing a stale graph

package/core/audit.mjs

@@ -160,7 +160,9 @@ export function audit(repo, cfg, res) {
     if (!DOC_EXT.test(f)) continue;
     const owners = graph.entities.filter((e) => {
       const d = e.derived || {};
-      return (d.docs || []).includes(f) || (d.constraints || []).includes(f) || (d.runbooks || []).includes(f);
+      const context = e.entity.spec?.context || {};
+      return [d, context].some((c) =>
+        ["docs", "constraints", "runbooks"].some((key) => (c[key] || []).includes(f)));
     }).map((e) => e.ref);
     const role = (configured.find((h) => h.path === f) || {}).role || null;
     docInventory.push({ path: f, linkedTo: owners.sort(), role });
@@ -193,9 +195,9 @@ export function audit(repo, cfg, res) {
       subject: d.path,
       refs: [d.path],
       message:
-        "document is claimed by no component" +
+        "document is claimed by no entity" +
         (d.role ? " and its configured role (" + d.role + ") is not a repository-wide role" : "") +
-        ". Link it from a component descriptor, or remove it.",
+        ". Link it from an entity descriptor, or remove it.",
     });
   }
   for (const h of hierarchyDocs) {

package/core/codes.mjs

@@ -77,6 +77,9 @@ export const CODES = {
   WARNING_ACCEPTANCE: "AGENTDOC_WARNING_ACCEPTANCE",
   OVERRIDE_STALE: "AGENTDOC_OVERRIDE_STALE",
   JOURNEY: "AGENTDOC_JOURNEY",
+
+  // language manifests
+  PYTHON_SPECIFIER: "AGENTDOC_PYTHON_SPECIFIER",
 };
 
 // Warning codes that a reviewer may explicitly accept. Anything outside this
@@ -94,6 +97,7 @@ export const ACCEPTABLE_WARNING_CODES = Object.freeze([
   "AGENTDOC_VERIFICATION_UNTIERED",
   "AGENTDOC_NORMATIVE_UNCOVERED",
   "AGENTDOC_REQUIREMENT_UNVERIFIED",
+  "AGENTDOC_PYTHON_SPECIFIER",
 ]);
 
 export class AgentDocError extends Error {

package/core/compile.mjs

@@ -17,11 +17,13 @@ import { redactCommand } from "./secrets.mjs";
 import { formatErrors } from "./jsonschema.mjs";
 import { validateContractFile } from "./contracts.mjs";
 import { sourceFiles, importSpecifiers } from "./sourcescan.mjs";
+import { readPythonUnit, pythonImportNames } from "../adapters/python.mjs";
 import { applyWarningAcceptances } from "./acceptances.mjs";
 import {
   loadNormativeDocuments, verifyCitation, normativeCoverage, isNormative, isRequirementKey, NORMATIVE_SEMANTICS_PREFIX,
 } from "./normative.mjs";
 import { loadAdapters } from "../adapters/index.mjs";
+import { loadCargoUnit, analyzeCargoDeps, rustIdentsInSource } from "../adapters/rust.mjs";
 import {
   COMPILER_NAME, COMPILER_VERSION, GRAPH_SCHEMA_VERSION,
   assembleGraph, serializeGraph, finalizeSerialization, subjectResolver,
@@ -130,11 +132,6 @@ export function compile(root, opts = {}) {
   for (const api of sources.entities.filter((e) => e.kind === "API")) {
     collect(() => validateContractFile(repo, bundle, api), res.errors);
   }
-  res.errors.push(...validateOidcProviders({ repo, sources, discovery: null }));
-
-  if (res.errors.length) {
-    return earlyOut(res, { entities: sources.entities.length });
-  }
 
   let adapters;
   try {
@@ -147,16 +144,22 @@ export function compile(root, opts = {}) {
     throw e;
   }
   const discovery = discoverUnits(repo, cfg, adapters);
+  repo.nestedUnitRoots = discovery.nestedRoots;
   // Eligibility is the compiler's own answer to "which directories are units" —
   // exposed on the result so scaffold can write descriptors for exactly these
   // roots rather than re-deriving them from filesystem markers.
   res.discovery = discovery;
-  const match = matchComponents(discovery.eligible, sources.entities.filter((e) => e.kind === "Component"));
-  res.errors.push(...match.errors);
 
-  // OIDC discovery must be exposed by the provider's own source. Re-check now
-  // that component -> unit bindings are known.
+  // A provider descriptor sits at its unit root. Check its source only after
+  // ownership is known, while still reporting this error alongside other
+  // descriptor/contract errors rather than hiding it behind an early return.
   res.errors.push(...validateOidcProviders({ repo, sources, discovery }));
+  if (res.errors.length) {
+    return earlyOut(res, { entities: sources.entities.length });
+  }
+
+  const match = matchComponents(discovery.eligible, sources.entities.filter((e) => e.kind === "Component"), cfg);
+  res.errors.push(...match.errors);
 
   if (res.errors.length) {
     return earlyOut(res, { entities: sources.entities.length, units: discovery.eligible.length });
@@ -285,6 +288,17 @@ export function compile(root, opts = {}) {
   // ── manifest pre-pass: identify each unit's package / module namespace ────
   // Done before extraction so cross-unit resolution never depends on the order
   // in which units happen to be processed.
+  // Cargo.toml is read only when the rust adapter is on. An existence probe is
+  // part of the input hash, so probing it for every unit would change every
+  // graph that does not enable rust.
+  const rustOn = adapters.some((a) => a.name === "rust");
+  ctx.unitByCrateName = new Map();
+  ctx.ambiguousCrateNames = new Map();
+  ctx.rustAmbiguity = new Map();
+  // A Python manifest is read only when the python adapter is on. An existence
+  // probe is part of the input hash, so probing one for every unit would change
+  // every graph that does not enable python.
+  const pythonOn = adapters.some((a) => a.name === "python");
   for (const unit of discovery.eligible) {
     const pkgPath = unit.root + "/package.json";
     if (repo.exists(pkgPath)) {
@@ -301,15 +315,68 @@ export function compile(root, opts = {}) {
       const m = /^module\s+(\S+)/m.exec(repo.readText(gomodPath));
       unit.goModule = m ? m[1] : null;
     }
+    if (rustOn) loadCargoUnit(repo, unit);
+    if (pythonOn) {
+      const py = readPythonUnit(repo, unit.root);
+      if (py.manifest) {
+        unit.pythonMarker = py.manifest;
+        unit.pythonManifest = py.manifest;
+        unit.pythonDist = py.dist;
+        unit.pythonImports = py.ambiguousImports ? null : py.importNames;
+        unit.pythonProdDeps = [...new Set([
+          ...py.prodDeps,
+          ...py.sourceDeps.filter((n) => !py.devDeps.includes(n) && !py.prodDeps.includes(n)),
+        ])].sort();
+        unit.pythonDevDeps = py.devDeps;
+        unit.pythonPathDeps = py.pathDeps;
+        if (py.error) res.errors.push(py.error);
+      }
+    }
   }
   const unitByPkgName = new Map();
   const unitByGoModule = new Map();
+  const unitByPythonDist = new Map();
+  const unitByPythonImport = new Map();
+  const distOwners = new Map();
+  const importOwners = new Map();
   for (const unit of discovery.eligible) {
     if (unit.pkgName && !unitByPkgName.has(unit.pkgName)) unitByPkgName.set(unit.pkgName, unit);
     if (unit.goModule && !unitByGoModule.has(unit.goModule)) unitByGoModule.set(unit.goModule, unit);
+    if (unit.pythonDist) {
+      if (!distOwners.has(unit.pythonDist)) distOwners.set(unit.pythonDist, []);
+      distOwners.get(unit.pythonDist).push(unit);
+    }
+    if (Array.isArray(unit.pythonImports)) {
+      for (const name of unit.pythonImports) {
+        if (!importOwners.has(name)) importOwners.set(name, []);
+        importOwners.get(name).push(unit);
+      }
+    }
+  }
+  for (const [name, owners] of distOwners) {
+    if (owners.length === 1) unitByPythonDist.set(name, owners[0]);
+    else for (const u of owners) u.pythonDistConflict = true;
+  }
+  for (const [name, owners] of importOwners) {
+    if (owners.length === 1) unitByPythonImport.set(name, owners[0]);
+    else for (const u of owners) u.pythonImportConflict = true;
   }
   ctx.unitByPkgName = unitByPkgName;
   ctx.unitByGoModule = unitByGoModule;
+  if (rustOn) {
+    const owners = new Map();
+    for (const unit of discovery.eligible) {
+      if (!unit.crateName) continue;
+      if (!owners.has(unit.crateName)) owners.set(unit.crateName, []);
+      owners.get(unit.crateName).push(unit);
+    }
+    for (const [name, list] of [...owners.entries()].sort((a, b) => (a[0] < b[0] ? -1 : 1))) {
+      if (list.length === 1) ctx.unitByCrateName.set(name, list[0]);
+      else ctx.ambiguousCrateNames.set(name, list.slice().sort((a, b) => (a.root < b.root ? -1 : 1)));
+    }
+  }
+  ctx.unitByPythonDist = unitByPythonDist;
+  ctx.unitByPythonImport = unitByPythonImport;
 
   // Manifest-declared unit dependencies, computed before any adapter runs so
   // that cross-unit reasoning never depends on adapter execution order.
@@ -317,6 +384,7 @@ export function compile(root, opts = {}) {
   // matches a dependency name rather than a blob of source.
   const productionDependencies = new Map();
   const dependencyMap = new Map();
+  const unitsByRoot = new Map(discovery.eligible.map((u) => [u.root, u]));
   for (const unit of discovery.eligible) {
     if (!unit.component) continue;
     const deps = new Set();
@@ -338,6 +406,32 @@ export function compile(root, opts = {}) {
         if (t && t.component && t.component.ref !== unit.component.ref) deps.add(t.component.ref);
       }
     }
+    if (rustOn && unit.cargoPackage) {
+      const cargo = analyzeCargoDeps(unit, unitsByRoot);
+      productionDependencies.set(unit.component.ref, [
+        ...(productionDependencies.get(unit.component.ref) || []),
+        ...cargo.prodNames,
+      ]);
+      for (const hit of cargo.resolved) {
+        if (hit.ambiguous || !hit.target || !hit.target.component) continue;
+        if (hit.target.component.ref !== unit.component.ref) deps.add(hit.target.component.ref);
+      }
+    }
+    if (unit.pythonMarker) {
+      const pyNames = [...new Set([...(unit.pythonProdDeps || []), ...(unit.pythonDevDeps || [])])];
+      productionDependencies.set(unit.component.ref, [
+        ...(productionDependencies.get(unit.component.ref) || []),
+        ...(unit.pythonProdDeps || []),
+      ]);
+      for (const name of pyNames) {
+        const t = unitByPythonDist.get(name);
+        if (t && t.component && t.component.ref !== unit.component.ref) deps.add(t.component.ref);
+      }
+      for (const p of unit.pythonPathDeps || []) {
+        const t = discovery.eligible.find((u) => u.root === p.dir);
+        if (t && t.component && t.component.ref !== unit.component.ref) deps.add(t.component.ref);
+      }
+    }
     dependencyMap.set(unit.component.ref, deps);
   }
   ctx.dependencyMap = dependencyMap;
@@ -942,9 +1036,13 @@ const GO_IMPORT_RE = /["`]([a-z0-9]+\.[a-z0-9.-]+\/[a-z0-9./_-]+|[a-z0-9]+\.[a-z
 function buildImportIndex(repo, discovery) {
   const byUnit = new Map();
   const goPathsByUnit = new Map();
+  const rustIdentsByUnit = new Map();
+  const pythonImportsByUnit = new Map();
   for (const unit of discovery.eligible) {
     const map = new Map();
     const goPaths = new Set();
+    const rustIdents = new Map();
+    const pyImports = new Map();
     for (const f of sourceFiles(repo, unit.root, { test: false })) {
       const specifiers = importSpecifiers(repo.readText(f));
       for (const s of specifiers) {
@@ -958,11 +1056,26 @@ function buildImportIndex(repo, discovery) {
         // importing it, with no require line at all.
         for (const m of text.matchAll(GO_IMPORT_RE) ) goPaths.add(m[1]);
       }
+      if (unit.cargoPackage && f.endsWith(".rs")) {
+        const text = repo.readText(f);
+        for (const ident of rustIdentsInSource(text)) {
+          if (!rustIdents.has(ident)) rustIdents.set(ident, new Set());
+          rustIdents.get(ident).add(f);
+        }
+      }
+      if (unit.pythonMarker && f.endsWith(".py")) {
+        for (const name of pythonImportNames(repo.readText(f))) {
+          if (!pyImports.has(name)) pyImports.set(name, new Set());
+          pyImports.get(name).add(f);
+        }
+      }
     }
     byUnit.set(unit, map);
     goPathsByUnit.set(unit, goPaths);
+    rustIdentsByUnit.set(unit, rustIdents);
+    pythonImportsByUnit.set(unit, pyImports);
   }
-  return { byUnit, goPathsByUnit };
+  return { byUnit, goPathsByUnit, rustIdentsByUnit, pythonImportsByUnit };
 }
 
 function mergeDerived(target, extra) {
@@ -995,7 +1108,7 @@ function validateOidcProviders({ repo, sources, discovery }) {
     const roots = unit ? [unit.root] : [dirOf(provider.file)];
     let found = false;
     for (const root of roots) {
-      for (const f of repo.walk(root)) {
+      for (const f of repo.walkUnit(root)) {
         if (!/\.(ts|tsx|js|mjs|jsx|py|go|rb|java|kt|rs)$/.test(f)) continue;
         if (/(^|\/)(test|tests|__tests__)\//.test(f) || /\.(test|spec)\./.test(f)) continue;
         if (repo.readText(f).includes(dp)) { found = true; break; }

package/core/dependents.mjs

@@ -0,0 +1,42 @@
+// Change routing follows dependency edges in reverse. Normalize inverse edges
+// here so query and impact agree even when the graph includes both spellings.
+export function dependentScope(graph, seeds) {
+  const reverse = new Map();
+  for (const r of graph.relations) {
+    let dependency, dependent;
+    if (r.type === "buildDependsOn" || r.type === "testDependsOn") {
+      dependency = r.targetRef;
+      dependent = r.sourceRef;
+    } else if (r.type === "buildDependencyOf" || r.type === "testDependencyOf") {
+      dependency = r.sourceRef;
+      dependent = r.targetRef;
+    } else continue;
+    if (!reverse.has(dependency)) reverse.set(dependency, []);
+    reverse.get(dependency).push({ ref: dependent, unitOnly: r.type.startsWith("test") });
+  }
+
+  // false means all tiers; true means only unit checks. An all-build route
+  // upgrades a prior test-only route, including its downstream dependents.
+  const scope = new Map(seeds.map((ref) => [ref, false]));
+  const queue = [...scope.keys()];
+  for (let i = 0; i < queue.length; i++) {
+    const current = queue[i];
+    for (const edge of reverse.get(current) || []) {
+      const unitOnly = scope.get(current) || edge.unitOnly;
+      if (!scope.has(edge.ref) || (scope.get(edge.ref) && !unitOnly)) {
+        scope.set(edge.ref, unitOnly);
+        queue.push(edge.ref);
+      }
+    }
+  }
+  return scope;
+}
+
+export function verificationForChange(graph, seeds, priorityRefs = seeds) {
+  const own = new Set(priorityRefs);
+  const scope = dependentScope(graph, seeds);
+  const rank = (v) => v.componentRefs.some((ref) => own.has(ref)) ? 0 : 1;
+  return graph.verification
+    .filter((v) => v.componentRefs.some((ref) => scope.has(ref) && (!scope.get(ref) || v.tier === "unit")))
+    .sort((a, b) => rank(a) - rank(b) || (a.id < b.id ? -1 : a.id > b.id ? 1 : 0));
+}

package/core/discover.mjs

@@ -8,12 +8,22 @@ import path from "node:path";
 import { AgentDocError, CODES } from "./codes.mjs";
 import { expandGlob, globToRegExp, assertGlob } from "../core/fsx.mjs";
 
-// Directories that are never units. Overridable, because "infra" or "tools"
-// may be a legitimate unit in another project.
+// Roots excluded from inference and scaffolding. Authored descriptors strictly
+// below them can still claim units; descriptors at these exact roots cannot.
 export const DEFAULT_NOT_UNIT_ROOTS = ["agentdoc", "docs", "scripts", "node_modules", ".github"];
 
+function notUnitRoots(cfg) {
+  return cfg?.discovery.notUnitRoots || DEFAULT_NOT_UNIT_ROOTS;
+}
+
+// Inference excludes the whole subtree, not similarly named siblings. CREATE
+// mode shares this policy even for units with an existing authored descriptor.
+export function isNotUnitRoot(root, cfg) {
+  return notUnitRoots(cfg)
+    .some((excluded) => root === excluded || root.startsWith(excluded + "/"));
+}
+
 export function discoverUnits(repo, cfg, adapters) {
-  const notUnit = new Set(cfg.discovery.notUnitRoots || DEFAULT_NOT_UNIT_ROOTS);
   const extraDeployable = new Set();
   const extraImportable = new Set();
   const units = new Map();
@@ -35,13 +45,17 @@ export function discoverUnits(repo, cfg, adapters) {
     assertGlob(g, "agentdoc config");
     for (const f of expandGlob(repo, g)) {
       const dir = path.posix.dirname(f);
-      if (!notUnit.has(dir) && repo.isDir(dir)) {
+      if (repo.isDir(dir)) {
         candidates.add(dir);
         descriptorRoots.add(dir);
       }
     }
   }
-  for (const r of cfg.discovery.supplementalRoots || []) candidates.add(r);
+  for (const r of cfg.discovery.supplementalRoots || []) {
+    candidates.add(r);
+    // The descriptor loader also reads these fixed paths outside the globs.
+    if (repo.exists(r + "/" + cfg.discovery.componentDescriptorName)) descriptorRoots.add(r);
+  }
 
   // Adapters may contribute roots the descriptor globs cannot know about: a
   // Go workspace member, a workspace file member with no descriptor yet. The
@@ -59,7 +73,10 @@ export function discoverUnits(repo, cfg, adapters) {
   }
 
   for (const root of [...candidates].sort()) {
-    if (notUnit.has(root)) continue;
+    // Preserve explicit human claims below an exclusion, while keeping inferred
+    // roots out of the subtree and refusing descriptors at the exact root.
+    if (notUnitRoots(cfg).includes(root)) continue;
+    if (isNotUnitRoot(root, cfg) && !descriptorRoots.has(root)) continue;
     if (!repo.isDir(root)) continue;
     const u = get(root);
     u.explicit = (cfg.discovery.supplementalRoots || []).includes(root) || descriptorRoots.has(root);
@@ -72,13 +89,38 @@ export function discoverUnits(repo, cfg, adapters) {
         const shape = markerShape(marker);
         if (shape === "deployable" || shape === "both") u.deployable = true;
         if (shape === "importable" || shape === "both") u.importable = true;
+        // A manifest with no artifact shape is still a unit. deployable and
+        // importable stay false, so scaffold does not invent a service or a
+        // library. A descriptor is not required before the unit is recognised.
+        if (shape === "present") u.present = true;
       }
     }
   }
 
   const list = [...units.values()].sort((a, b) => (a.root < b.root ? -1 : 1));
-  const eligible = list.filter((u) => u.deployable || u.importable || u.explicit);
-  return { units: list, eligible };
+  const eligible = list.filter((u) => u.deployable || u.importable || u.explicit || u.present);
+  // Only eligible units create ownership boundaries. Record immediate children
+  // once; pruning one of them also prunes every deeper descendant. Normalise
+  // the repository root so descriptor roots (".") and workspace roots agree.
+  const nestedRoots = new Map(eligible.map((u) => [unitRoot(u.root), new Set()]));
+  for (const root of nestedRoots.keys()) {
+    if (!root) continue;
+    let parent = unitRoot(path.posix.dirname(root));
+    while (true) {
+      if (nestedRoots.has(parent)) {
+        nestedRoots.get(parent).add(root);
+        break;
+      }
+      if (!parent) break;
+      parent = unitRoot(path.posix.dirname(parent));
+    }
+  }
+  return { units: list, eligible, nestedRoots };
+}
+
+function unitRoot(root) {
+  const normalized = path.posix.normalize(root || ".");
+  return normalized === "." ? "" : normalized;
 }
 
 function markerShape(marker) {
@@ -93,7 +135,7 @@ export function descriptorDir(file) {
 }
 
 // Exactly one descriptor per eligible unit, and no descriptor outside one.
-export function matchComponents(eligible, componentEntities) {
+export function matchComponents(eligible, componentEntities, cfg) {
   const errors = [];
   const byDir = new Map();
   for (const e of componentEntities) {
@@ -124,6 +166,15 @@ export function matchComponents(eligible, componentEntities) {
   for (const e of componentEntities) {
     const dir = descriptorDir(e.file);
     if (unitRoots.has(dir)) continue;
+    if (notUnitRoots(cfg).includes(dir)) {
+      errors.push(new AgentDocError(
+        CODES.COMPONENT_UNCORROBORATED,
+        "component descriptor at '" + dir + "' is in discovery.notUnitRoots (or a default not-unit root); " +
+          "remove it from notUnitRoots or move the descriptor",
+        { path: e.file, ref: e.ref }
+      ));
+      continue;
+    }
     // A descriptor is a human claim that a component exists. When no adapter
     // can corroborate a deployable or importable artifact in that source root,
     // the claim is unsupported. This is reported rather than ignored: it is

package/core/fsx.mjs

@@ -59,6 +59,7 @@ export class Repo {
     this.probes = new Map();
     this.walks = new Map();
     this.listings = new Map();
+    this.nestedUnitRoots = new Map();
     this.generatedDirs = new Set(opts.generatedDirs || DEFAULT_GENERATED_DIRS);
     this.noGit = Boolean(opts.noGit);
   }
@@ -140,6 +141,22 @@ export class Repo {
     this.walks.set(relDir || ".", out);
     return out;
   }
+  // Per-unit scans use the discovery result, never filesystem heuristics.
+  // Keep walk() repository-wide for discovery, contracts and authored inputs.
+  ownsUnitPath(unitRoot, rel) {
+    const normalize = (p) => path.posix.normalize(p || ".").replace(/^\.$/, "");
+    const root = normalize(unitRoot);
+    const target = normalize(rel);
+    if (root && target !== root && !target.startsWith(root + "/")) return false;
+    for (const child of this.nestedUnitRoots.get(root) || []) {
+      if (target === child || target.startsWith(child + "/")) return false;
+    }
+    return true;
+  }
+  walkUnit(unitRoot, relDir = unitRoot, { exclude = () => false } = {}) {
+    if (!this.ownsUnitPath(unitRoot, relDir)) return [];
+    return this.walk(relDir, { exclude: (rel, ent) => !this.ownsUnitPath(unitRoot, rel) || exclude(rel, ent) });
+  }
   // Files under a path or a path *prefix*. A contract is often named by a module
   // prefix rather than a single file (`events.go`, `events/*.go`), and
   // requiring an exact directory would reject a perfectly good contract.

package/core/graph.mjs

@@ -9,7 +9,7 @@ import { assertDeterministic, structuralProjection } from "./determinism.mjs";
 import { sha256Hex } from "./fsx.mjs";
 
 export const COMPILER_NAME = "agentdoc-compiler";
-export const COMPILER_VERSION = "1.1.0";
+export const COMPILER_VERSION = "1.2.0";
 export const GRAPH_SCHEMA_VERSION = "agentdoc.dev/graph/v1";
 
 // Resolve symbolic provenance subjects to RFC 6901 pointers into the graph.