@phyzess/pappra 0.1.0-beta.10 → 0.1.0-beta.11

package/README.md

@@ -64,7 +64,7 @@ They are not needed for the core workflow above.
 - **Workspace configuration:** `.pappra/workspace.json` and checkout-local `.pappra/local/machine.json`.
 - **Knowledge:** workspace and private document catalogs with explicit preview/apply operations.
 - **Continuity:** private task checkpoints and bounded advisory resume packets. Resume never grants execution by itself.
-- **Code intelligence:** status, explicit preparation and bounded query for selected repositories. Text/structure fallback is available when the optional graph engine is absent.
+- **Code intelligence:** status, explicit preparation and bounded query for selected repositories. Text/structure fallback is available when the optional graph engine is absent. Registrations are stored under the workspace `.pappra/local/code`, never inside a repository checkout, so a multi-repository workspace does not turn its checkouts into nested workspaces.
 - **Host integrations:** optional Pi, Codex and Claude Code adapters that merge Pappra-owned entries without taking over user configuration. Hooks are copied as a dependency-free bundle; Claude Code uses `${CLAUDE_PROJECT_DIR}` and Pi imports its runtime relatively, while Codex 0.163.0 loads hooks only from `$CODEX_HOME/hooks.json` (`host install --host codex --scope user`). `host bundle --marketplace` exports a marketplace that Claude Code and Codex accept without registering it. Plugin hooks are verified for Pi 1.3.0 and Claude Code 2.1.292 (startup) and unsupported for Codex, so `host install --mode plugin` fails closed with the per-host registration commands. See [host plugin validation](docs/host-plugin-validation.md).
 - **Bounded collaboration:** an optional, explicitly controlled one-request workflow. It is not a scheduler or daemon.
 
@@ -89,7 +89,7 @@ The check runs the source policy, type checks, formatting, deterministic tests a
 
 ## Status and limits
 
-Pappra is development software (`0.1.0-beta.10`) published as `@phyzess/pappra` under the `beta` dist-tag. Releases are published from GitHub Actions with npm trusted publishing (OIDC), so no npm token is stored in this repository. Pin either the moving `beta` tag or an exact version such as `@phyzess/pappra@0.1.0-beta.10`, because pre-release versions are never republished.
+Pappra is development software (`0.1.0-beta.11`) published as `@phyzess/pappra` under the `beta` dist-tag. Releases are published from GitHub Actions with npm trusted publishing (OIDC), so no npm token is stored in this repository. Pin either the moving `beta` tag or an exact version such as `@phyzess/pappra@0.1.0-beta.11`, because pre-release versions are never republished.
 
 The deterministic suite covers synthetic workspaces, fixtures and local process boundaries. It does not establish real-model behavior, native host callability on every platform, CodeGraph completeness, Windows/Linux parity or production performance. A host adapter version pin is an observed support claim, not proof that a particular native installation will load or run correctly.
 

package/dist/app/doctor.js

@@ -886,14 +886,33 @@ export async function runDoctor(options = {}) {
         ],
     }));
     const selectedHosts = machine?.selectedHosts ?? [];
-    const hostRootBase = root ?? homeDir;
+    // Passive observation only: a host install can target the private default root, a
+    // project directory, or Codex's user configuration directory.
+    const hostInstallRoots = (host) => {
+        const roots = [
+            join(root ?? homeDir, '.pappra', 'local', 'hosts', host),
+            join(root ?? homeDir, `.${host}`),
+        ];
+        if (host === 'codex') {
+            roots.push(process.env['CODEX_HOME'] ?? join(homeDir, '.codex'));
+        }
+        return roots;
+    };
     const installedHostBundle = (await Promise.all(selectedHosts.map(async (host) => {
-        const path = join(hostRootBase, '.pappra', 'local', 'hosts', host, 'pappra-host.json');
-        return (await observePath(path)).kind === 'file' ? path : null;
+        for (const base of hostInstallRoots(host)) {
+            const path = join(base, 'pappra-host.json');
+            if ((await observePath(path)).kind === 'file')
+                return path;
+        }
+        return null;
     }))).find((path) => path !== null) ?? null;
     const installedHostSkill = (await Promise.all(selectedHosts.map(async (host) => {
-        const path = join(hostRootBase, '.pappra', 'local', 'hosts', host, 'skills', 'pappra', 'SKILL.md');
-        return (await observePath(path)).kind === 'file' ? path : null;
+        for (const base of hostInstallRoots(host)) {
+            const path = join(base, 'skills', 'pappra', 'SKILL.md');
+            if ((await observePath(path)).kind === 'file')
+                return path;
+        }
+        return null;
     }))).find((path) => path !== null) ?? null;
     checks.push(...hostChecks(selectedHosts, homeDir, pathEnv, observedAt));
     checks.push(makeCheck({

package/dist/code/service.js

@@ -177,7 +177,10 @@ async function observeCode(input) {
         : fallbackHealth('unsupported', raw.code, versionValue);
     if (!raw.ok)
         diagnostics.push(outcomeDiagnostic(raw, repository.root));
-    const registrationRead = await readCodeRegistration(repository.root, input.repositoryId);
+    // Registrations belong to the workspace, not to a repository checkout: writing
+    // <repo>/.pappra/local/code would make that checkout look like a nested workspace
+    // and hide it from the outer workspace discovery.
+    const registrationRead = await readCodeRegistration(input.root, input.repositoryId);
     let registration = null;
     let registrationFailure = null;
     if (registrationRead.ok) {
@@ -193,7 +196,7 @@ async function observeCode(input) {
         rawHealth,
         health,
         registration,
-        registrationPath: codeRegistrationPath(repository.root, input.repositoryId),
+        registrationPath: codeRegistrationPath(input.root, input.repositoryId),
         excludedRoots,
         access: repository.access,
         diagnostics,
@@ -345,9 +348,12 @@ export class CodeIntelligenceService {
                 diagnostics: [...observed.diagnostics],
             };
         }
-        const registrationTarget = codeRegistrationPath(observed.identity.root, observed.identity.repositoryId);
-        for (const target of [plan.indexPath, registrationTarget]) {
-            const boundary = await ensureCodeMutationBoundary(observed.identity.root, target, observed.excludedRoots);
+        const registrationTarget = codeRegistrationPath(input.root, observed.identity.repositoryId);
+        const boundaries = await Promise.all([
+            ensureCodeMutationBoundary(observed.identity.root, plan.indexPath, observed.excludedRoots),
+            ensureCodeMutationBoundary(input.root, registrationTarget),
+        ]);
+        for (const boundary of boundaries) {
             if (!boundary.ok) {
                 return {
                     schema: 'pappra/code-prepare-result/1',
@@ -364,12 +370,12 @@ export class CodeIntelligenceService {
                     registrationPath: null,
                     diagnostics: [
                         ...observed.diagnostics,
-                        outcomeDiagnostic(boundary, target),
+                        outcomeDiagnostic(boundary, registrationTarget),
                     ],
                 };
             }
         }
-        const lock = await acquireCodePrepareLock(observed.identity.root, observed.excludedRoots);
+        const lock = await acquireCodePrepareLock(input.root);
         if (!lock.ok) {
             return {
                 schema: 'pappra/code-prepare-result/1',
@@ -507,7 +513,7 @@ export class CodeIntelligenceService {
                 preparedAt: new Date().toISOString(),
                 coverage: prepared.value.coverage,
             };
-            const written = await writeCodeRegistration(afterIdentity.value.root, registration, observed.excludedRoots);
+            const written = await writeCodeRegistration(input.root, registration);
             if (!written.ok) {
                 return {
                     schema: 'pappra/code-prepare-result/1',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phyzess/pappra",
-  "version": "0.1.0-beta.10",
+  "version": "0.1.0-beta.11",
   "description": "Portable workspace knowledge and continuity for coding agents.",
   "publishConfig": {
     "access": "public"