codenib 0.2.1__tar.gz → 0.2.3__tar.gz

{codenib-0.2.1 → codenib-0.2.3}/CHANGELOG.md

@@ -11,6 +11,101 @@ All notable user-facing changes are recorded here. CodeNib follows
 
 ## [Unreleased]
 
+## [0.2.3] - 2026-09-03
+
+### Added
+
+- A Wiki-only `codenib.storage` facade exposing the domain-local `WikiStore`
+  harness and SQLite WAL implementation, with versioned schema initialization,
+  bounded canonical JSON, integrity checks, atomic publication, and
+  cross-process generation guards.
+
+### Changed
+
+- AgentWiki, the web service, cache audit, prewarming, and Wiki benchmarking
+  now use `wiki_cache/wiki.sqlite3`. Eligible source-compatible JSON entries
+  remain available through read-through compatibility and are not rewritten or
+  deleted.
+- The supported product database boundary is now
+  `codenib.storage.WikiStore`, with `SQLiteWikiStore` as its supported adapter.
+  `RepoManifest`, BM25, FAISS, igraph, and portable context payloads remain file
+  artifacts. Existing compiler caches use `artifact pack`; portable artifacts
+  continue through `artifact verify` and `mcp --artifact`.
+- The v0.2.3 release intentionally narrows the former storage API and CLI.
+  Users who still need data from a v0.2.2 SQLite catalog must run `artifact
+  materialize` with a pinned v0.2.2 environment before upgrading; the resulting
+  portable artifact remains supported.
+
+### Removed
+
+- The optional Web `index_storage` configuration and its catalog-backed local
+  runtime, retained BM25 activation, reconciliation, durable index-job
+  orchestration, `/api/index-jobs` write/read routes, and index-status job or
+  update-capability fields. Index status remains available as a read-only
+  `RepoManifest` projection.
+- The unreleased catalog-selected `codenib mcp` cold-start mode. Portable
+  artifacts remain served through `codenib mcp --artifact [--repo]`.
+- The unreleased `storage audit` command and `index --publish-retained` path.
+  Those two batches removed 1,407 production lines and 1,742 dedicated test
+  lines, including the audit execution path, eight index-only options, and
+  three compiler exports; ordinary indexing remained unchanged in that batch.
+- The post-v0.2.2 retained-storage benchmark gate, its manual Make target, and
+  noncanonical readiness receipt. The report-only experiment had no product or
+  CI workflow caller and could never report `promotion_eligible=true`; removing
+  it deleted a 4,913-line harness, 3,468 test lines, 367 evidence lines, 148
+  documentation lines, eight Make variables, and one manual target.
+- The unreleased `codenib jobs` execution stack and catalog schema v5 through
+  v8. This removed eight production modules (9,615 lines), twelve dedicated
+  test modules (22,170 lines), 73 lazy exports, two interruptible CAS methods,
+  one command with two execution paths, and four schema migrations; changes
+  inside retained files bring the batch total to 21,214 production and 29,352
+  test lines removed.
+- The generic retained-storage surface formerly published by v0.2.2 through
+  `codenib.storage`: its schema-v4 SQLite catalog and local CAS, `artifact
+  import-cache`, `artifact materialize`, and the retained compiler bridge. The
+  name `codenib.storage` now resolves only to the Wiki database facade. Normal
+  index, Wiki, portable-artifact, publish, and MCP paths are unchanged.
+- The catalog-backed clangd FactBatch publication/reuse experiment and its
+  profiling target. Provider-neutral FactBatch models, resolvers, native buffer
+  transport, and the promoted clangd query index remain independent of storage.
+
+## [0.2.2] - 2026-08-21
+
+### Added
+
+- Persistent, exact repository-relative source exclusions through
+  `--exclude-dir` and `--clear-exclude-dirs`, with one recorded policy reused
+  by CodeGraph, indexing, MCP, Wiki, Web, and public compiler entry points.
+- Manifest 1.2 source-selection identities and builder receipts, while retaining
+  strict read compatibility for manifest 1.1 artifacts.
+- Authenticated optional SCIP occurrence-sidecar receipts bound to the same
+  owned symbol-graph generation as `graph.pkl`.
+
+### Changed
+
+- Authenticated indexing now accepts absolute symbolic links only when their
+  lexical target remains inside the same pinned repository authority. Expo,
+  CocoaPods, and pnpm-style contained link layouts no longer require a broad
+  default-ignore rule.
+- CodeGraph status reports the effective source selection, and Wiki, publish,
+  doctor, and toolchain flows reuse it instead of silently widening the source
+  surface.
+- Manifest-bound C and C++ queries temporarily use the verified persisted
+  symbol graph instead of consuming project-local clangd postings directly.
+
+### Security
+
+- Source paths, graph artifacts, native query routes, and retained manifests
+  are checked against the same authenticated source selection before they can
+  be published or served. Unproven native routes fail closed to the persisted
+  graph.
+- Zoekt builds use a fixed commit-tree contract, private generation
+  publication, and an authenticated shard-tree receipt; custom exclusions are
+  rejected until the backend can prove that narrower surface end to end.
+- Authenticated MCP `search_zoekt` serving uses a retained Linux `/proc`
+  descriptor snapshot. Other platforms fail closed until they have an
+  equivalent immutable runtime handoff.
+
 ## [0.2.1] - 2026-08-14
 
 ### Added
@@ -156,7 +251,9 @@ All notable user-facing changes are recorded here. CodeNib follows
 - Prepared secretless PyPI publishing through a dedicated GitHub Actions OIDC
   workflow.
 
-[Unreleased]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.1...HEAD
+[Unreleased]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.3...HEAD
+[0.2.3]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.2...v0.2.3
+[0.2.2]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.1...v0.2.2
 [0.2.1]: https://github.com/sysevol-ai/CodeNib/compare/v0.2.0...v0.2.1
 [0.2.0]: https://github.com/sysevol-ai/CodeNib/compare/v0.1.0...v0.2.0
 [0.2.0a2]: https://github.com/sysevol-ai/CodeNib/compare/620a82d...78e12ac

{codenib-0.2.1 → codenib-0.2.3}/MANIFEST.in

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: Apache-2.0
 
 graft web
+include native/workspace_owner.c
 include CHANGELOG.md
 include CONTRIBUTING.md
 include server.json

{codenib-0.2.1 → codenib-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: codenib
-Version: 0.2.1
+Version: 0.2.3
 Summary: A multi-view data system for serving repository context to coding agents
 Author-email: Zhongming Yu <zhy025@ucsd.edu>
 License-Expression: Apache-2.0
@@ -133,6 +133,8 @@ SPDX-License-Identifier: Apache-2.0
     &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/">Documentation</a>
     &nbsp;&middot;&nbsp;
+    <a href="https://docs.codenib.ai/news/">News</a>
+    &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/codegraph/">CodeGraph</a>
     &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/mcp/">MCP</a>
@@ -143,15 +145,16 @@ SPDX-License-Identifier: Apache-2.0
   </p>
   <p>
     <a href="https://github.com/sysevol-ai/CodeNib/actions/workflows/ci-full.yml"><img src="https://github.com/sysevol-ai/CodeNib/actions/workflows/ci-full.yml/badge.svg" alt="CI"></a>
-    <a href="https://pypi.org/project/codenib/"><img src="https://img.shields.io/pypi/v/codenib.svg" alt="PyPI version"></a>
+    <a href="https://pypi.org/project/codenib/"><img src="https://img.shields.io/pypi/v/codenib.svg?cacheSeconds=300" alt="PyPI version"></a>
+    <a href="https://docs.codenib.ai/codegraph/#one-command-setup"><img src="https://img.shields.io/badge/Claude_Code-D97757?logo=claude&amp;logoColor=fff" alt="Claude Code supported"></a>
+    <a href="https://docs.codenib.ai/codegraph/#one-command-setup"><img src="https://img.shields.io/badge/Codex-000?logo=openai&amp;logoColor=fff" alt="Codex supported"></a>
     <a href="https://github.com/sysevol-ai/CodeNib/blob/main/LICENSE"><img src="https://img.shields.io/badge/License-Apache_2.0-blue.svg" alt="License: Apache 2.0"></a>
     <a href="https://github.com/sysevol-ai/CodeNib/blob/main/pyproject.toml"><img src="https://img.shields.io/badge/Python-3.10%2B-3776AB.svg" alt="Python 3.10+"></a>
-    <img src="https://img.shields.io/badge/Release-0.2.1-2563EB.svg" alt="CodeNib 0.2.1">
   </p>
 </div>
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.1"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/your/repo
 ```
 
@@ -161,58 +164,27 @@ symbol graph, and registers the resulting MCP server with installed Codex and
 Claude Code clients. It is local, open source, requires no model or cloud, and
 does not write configuration or indexes into the target repository.
 
-## News
-
-- **2026-08-13 — CodeNib 0.2.1 CodeGraph onboarding.** One command prepares a
-  repository graph and connects it to Codex and Claude Code, with idempotent
-  status, safe uninstall, and installed-wheel MCP graph verification.
-  [CodeGraph guide](https://docs.codenib.ai/codegraph/)
-- **2026-08-08 — RepoNavigator Jump adapter.** The published single-tool
-  [RepoNavigator](https://arxiv.org/abs/2512.20957v6) contract now resolves
-  symbol definitions through a persisted SCIP occurrence or injected LSP
-  signal, with graph-only resolution disclosed as a degraded fallback.
-  [Support boundary](https://docs.codenib.ai/agent_integrations/#reponavigator)
-- **2026-08-05 — CodeNib 0.2.0.** Build a static Wiki and reusable context
-  artifact once, then serve it through Pages or the official MCP package.
-  Hybrid retrieval and managed SCIP/LSP providers ship in the same CLI.
-  [Release notes](https://docs.codenib.ai/releases/0.2.0/)
-- **2026-08-05 — SweRank recipe.** Run
-  [SweRank](https://github.com/SalesforceAIResearch/SweRank) retrieval and
-  reranking over a local checkout. [Example](examples/swerank_retrieve_rerank.py)
-- **2026-08-04 — Native repository explorer.** CodeNib's planner now targets
-  the [SWE-Explore](https://github.com/Qiushao-E/SWE-Explore-Bench)
-  source-region protocol.
-  [Validation](docs/evaluation/swe_explore.md)
-- **2026-08-03 — Native LocAgent policy.**
-  [LocAgent](https://github.com/gersteinlab/LocAgent) runs directly on CodeNib
-  views without LocAgent, LiteLLM, or LlamaIndex dependencies.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-- **2026-08-02 — OrcaLoca SearchAgent.**
-  [OrcaLoca](https://github.com/fishmingyu/OrcaLoca)'s six-tool search loop
-  now reuses CodeNib's symbol graph.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-
 ## System Architecture
 
 | Layer | Responsibility |
 |---|---|
-| Incremental compiler | Chunk source and materialize BM25, dense, graph, and navigation views; reuse or repair supported artifacts and rebuild when an update cannot be admitted |
+| View compiler | Chunk source and materialize BM25, dense, graph, and navigation views; reuse current artifacts and atomically rebuild affected views |
 | View manifest | Record repository identity, source fingerprint, builder profile, capabilities, status, and artifact location independently for each view |
 | Context serving | Execute lexical, semantic, hybrid, reranked, and structural query plans while preserving repository-relative source locations |
 | Agent runtime | Expose capability-aware MCP and LSP-shaped tools, assemble bounded evidence, and return citations that agents and humans can inspect |
 
 ```text
 repository change
-  -> materialize or repair affected views
+  -> reuse current views or rebuild affected views
   -> publish a capability-bearing manifest
   -> plan repository queries
   -> deliver bounded, source-linked context
 ```
 
-On a later commit, CodeNib can reuse unchanged vector content and patch
-supported graph transitions at file or symbol granularity. Unsupported,
-inconsistent, or unverified transitions fall back to a fresh build instead of
-publishing a partially updated view.
+On a later commit, CodeNib reuses views whose source and builder identities are
+still current. A requested view affected by source or policy changes currently
+rebuilds in an isolated generation; file- and symbol-level delta repair remains
+disabled until it can use the same pinned source authority.
 
 ## Quickstart
 
@@ -220,7 +192,7 @@ Requires Python 3.10+ and Git. For an agent-ready CodeGraph with no model or API
 key, install the graph and MCP extras and run one command:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.1"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -231,17 +203,40 @@ Run `codenib codegraph status /path/to/repository` to diagnose the complete
 path or `codenib codegraph uninstall /path/to/repository` to remove only the
 managed client registrations. The index remains reusable.
 
+Repositories can persist exact root-relative subtree exclusions when generated
+or vendored content should not be indexed:
+
+```bash
+codenib codegraph init /path/to/repository \
+  --exclude-dir ios/Pods \
+  --exclude-dir generated/api
+```
+
+Paths use repository-relative POSIX spelling (`/`) and name exact subtrees,
+not globs. Repeat `--exclude-dir` to replace the complete custom exclusion set. Later
+`init` and `index` runs reuse that policy from the manifest; use
+`--clear-exclude-dirs` to return to the default source surface. CodeNib does not
+implicitly treat `.gitignore` as an indexing policy, because tracked and local
+ignored source can still be intentional input.
+
+Zoekt supports the default source policy only when its fixed commit tree
+exactly matches the authenticated checkout and contains no tracked path that
+the default policy excludes. It does not currently support a non-empty custom
+exclusion set. A command that explicitly requests the `zoekt` view, including
+`--preset full`, fails closed when either condition is unmet; use the
+CodeGraph, `fast`, or semantic paths instead. Authenticated MCP serving for
+Zoekt currently requires Linux `/proc`; see the
+[source-surface boundaries](https://docs.codenib.ai/codegraph/#select-the-repository-source-surface).
+
 For a browser Wiki with hybrid BM25+dense retrieval, install the semantic extra:
 
 ```bash
-python -m pip install "codenib[semantic]==0.2.1"
+python -m pip install "codenib[semantic]"
 codenib wiki /path/to/repository
 ```
 
 Both paths keep reusable state under `~/.codenib/repositories` and leave the
-target checkout unchanged. Set `CODENIB_HOME` to relocate state. The
-[0.2.1 release notes](https://docs.codenib.ai/releases/0.2.1/) record the
-upgrade boundary and installed-product evidence.
+target checkout unchanged. Set `CODENIB_HOME` to relocate state.
 
 Preview the CodeGraph operations without installing, indexing, or configuring
 an agent:
@@ -255,7 +250,7 @@ only their package-level providers; operating-system and project prerequisites
 remain explicit:
 
 ```bash
-python -m pip install "codenib[graph]==0.2.1"
+python -m pip install "codenib[graph]"
 codenib toolchain install /path/to/repository --scope graph
 codenib doctor /path/to/repository --require graph
 ```
@@ -273,7 +268,7 @@ provider credential; interactive Ask and runtime graph exploration remain on
 the local or MCP serving path.
 
 For a repository-hosted Wiki, CodeNib also ships a reusable GitHub workflow
-that incrementally builds the same manifest, deploys the static site to Pages,
+that builds or reuses the same manifest, deploys the static site to Pages,
 and uploads the matching commit-addressed context artifact. Its default
 `semantic` route builds BM25 and vector views with a cached local Hugging Face
 model and needs no API key. An explicit `fast` route avoids the model download;
@@ -297,7 +292,7 @@ The recommended path configures installed Codex and Claude Code clients through
 their native CLIs:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.1"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -327,7 +322,7 @@ capabilities, loaded views, fusion, graph, and reranking trace.
 
 | Surface | Purpose |
 |---|---|
-| Incremental compiler | Build independently managed views, reuse unchanged content, repair supported transitions, and conservatively rebuild outside those boundaries |
+| View compiler | Build independently managed views, reuse current generations, and atomically rebuild changed views under one source identity |
 | Agent context runtime | Plan capability-aware retrieval and navigation, then assemble bounded source-linked evidence |
 | Retrieval | BM25, dense-vector, regex/trigram, Zoekt, fusion, and reranking paths; see the [validated model matrix](https://docs.codenib.ai/rag_ops/#validated-models) |
 | Structural context | SCIP/LSP-backed symbol graphs with source locations and typed edges |
@@ -376,8 +371,8 @@ running the credential- or toolchain-dependent tiers.
 
 ## Status
 
-CodeNib `0.1.0` is a developer preview. The CLI and manifest format are usable,
-but public interfaces may still change before a stable release. Historical
+CodeNib is currently in beta. The CLI and manifest format are usable, but
+public interfaces may still change before a stable release. Historical
 research artifacts retain their published dataset identifiers; the maintained
 package, import namespace, commands, and repository use `CodeNib`. See
 [Naming](https://docs.codenib.ai/branding/).
@@ -403,6 +398,8 @@ If you use CodeNib in your research, please cite our
 
 [Website](https://codenib.ai)
 &nbsp;&middot;&nbsp;
+[Releases](https://github.com/sysevol-ai/CodeNib/releases)
+&nbsp;&middot;&nbsp;
 [Changelog](https://github.com/sysevol-ai/CodeNib/blob/main/CHANGELOG.md)
 &nbsp;&middot;&nbsp;
 [Contributing](https://github.com/sysevol-ai/CodeNib/blob/main/CONTRIBUTING.md)

{codenib-0.2.1 → codenib-0.2.3}/README.md

@@ -24,6 +24,8 @@ SPDX-License-Identifier: Apache-2.0
      · 
     <a href="https://docs.codenib.ai/">Documentation</a>
     &nbsp;&middot;&nbsp;
+    <a href="https://docs.codenib.ai/news/">News</a>
+    &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/codegraph/">CodeGraph</a>
     &nbsp;&middot;&nbsp;
     <a href="https://docs.codenib.ai/mcp/">MCP</a>
@@ -34,15 +36,16 @@ SPDX-License-Identifier: Apache-2.0
   </p>
   <p>
     <a href="https://github.com/sysevol-ai/CodeNib/actions/workflows/ci-full.yml"><img src="https://github.com/sysevol-ai/CodeNib/actions/workflows/ci-full.yml/badge.svg" alt="CI"></a>
-    <a href="https://pypi.org/project/codenib/"><img src="https://img.shields.io/pypi/v/codenib.svg" alt="PyPI version"></a>
+    <a href="https://pypi.org/project/codenib/"><img src="https://img.shields.io/pypi/v/codenib.svg?cacheSeconds=300" alt="PyPI version"></a>
+    <a href="https://docs.codenib.ai/codegraph/#one-command-setup"><img src="https://img.shields.io/badge/Claude_Code-D97757?logo=claude&amp;logoColor=fff" alt="Claude Code supported"></a>
+    <a href="https://docs.codenib.ai/codegraph/#one-command-setup"><img src="https://img.shields.io/badge/Codex-000?logo=openai&amp;logoColor=fff" alt="Codex supported"></a>
     <a href="https://github.com/sysevol-ai/CodeNib/blob/main/LICENSE"><img src="https://img.shields.io/badge/License-Apache_2.0-blue.svg" alt="License: Apache 2.0"></a>
     <a href="https://github.com/sysevol-ai/CodeNib/blob/main/pyproject.toml"><img src="https://img.shields.io/badge/Python-3.10%2B-3776AB.svg" alt="Python 3.10+"></a>
-    <img src="https://img.shields.io/badge/Release-0.2.1-2563EB.svg" alt="CodeNib 0.2.1">
   </p>
 </div>
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.1"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/your/repo
 ```
 
@@ -52,58 +55,27 @@ symbol graph, and registers the resulting MCP server with installed Codex and
 Claude Code clients. It is local, open source, requires no model or cloud, and
 does not write configuration or indexes into the target repository.
 
-## News
-
-- **2026-08-13 — CodeNib 0.2.1 CodeGraph onboarding.** One command prepares a
-  repository graph and connects it to Codex and Claude Code, with idempotent
-  status, safe uninstall, and installed-wheel MCP graph verification.
-  [CodeGraph guide](https://docs.codenib.ai/codegraph/)
-- **2026-08-08 — RepoNavigator Jump adapter.** The published single-tool
-  [RepoNavigator](https://arxiv.org/abs/2512.20957v6) contract now resolves
-  symbol definitions through a persisted SCIP occurrence or injected LSP
-  signal, with graph-only resolution disclosed as a degraded fallback.
-  [Support boundary](https://docs.codenib.ai/agent_integrations/#reponavigator)
-- **2026-08-05 — CodeNib 0.2.0.** Build a static Wiki and reusable context
-  artifact once, then serve it through Pages or the official MCP package.
-  Hybrid retrieval and managed SCIP/LSP providers ship in the same CLI.
-  [Release notes](https://docs.codenib.ai/releases/0.2.0/)
-- **2026-08-05 — SweRank recipe.** Run
-  [SweRank](https://github.com/SalesforceAIResearch/SweRank) retrieval and
-  reranking over a local checkout. [Example](examples/swerank_retrieve_rerank.py)
-- **2026-08-04 — Native repository explorer.** CodeNib's planner now targets
-  the [SWE-Explore](https://github.com/Qiushao-E/SWE-Explore-Bench)
-  source-region protocol.
-  [Validation](docs/evaluation/swe_explore.md)
-- **2026-08-03 — Native LocAgent policy.**
-  [LocAgent](https://github.com/gersteinlab/LocAgent) runs directly on CodeNib
-  views without LocAgent, LiteLLM, or LlamaIndex dependencies.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-- **2026-08-02 — OrcaLoca SearchAgent.**
-  [OrcaLoca](https://github.com/fishmingyu/OrcaLoca)'s six-tool search loop
-  now reuses CodeNib's symbol graph.
-  [Support matrix](https://docs.codenib.ai/agent_integrations/)
-
 ## System Architecture
 
 | Layer | Responsibility |
 |---|---|
-| Incremental compiler | Chunk source and materialize BM25, dense, graph, and navigation views; reuse or repair supported artifacts and rebuild when an update cannot be admitted |
+| View compiler | Chunk source and materialize BM25, dense, graph, and navigation views; reuse current artifacts and atomically rebuild affected views |
 | View manifest | Record repository identity, source fingerprint, builder profile, capabilities, status, and artifact location independently for each view |
 | Context serving | Execute lexical, semantic, hybrid, reranked, and structural query plans while preserving repository-relative source locations |
 | Agent runtime | Expose capability-aware MCP and LSP-shaped tools, assemble bounded evidence, and return citations that agents and humans can inspect |
 
 ```text
 repository change
-  -> materialize or repair affected views
+  -> reuse current views or rebuild affected views
   -> publish a capability-bearing manifest
   -> plan repository queries
   -> deliver bounded, source-linked context
 ```
 
-On a later commit, CodeNib can reuse unchanged vector content and patch
-supported graph transitions at file or symbol granularity. Unsupported,
-inconsistent, or unverified transitions fall back to a fresh build instead of
-publishing a partially updated view.
+On a later commit, CodeNib reuses views whose source and builder identities are
+still current. A requested view affected by source or policy changes currently
+rebuilds in an isolated generation; file- and symbol-level delta repair remains
+disabled until it can use the same pinned source authority.
 
 ## Quickstart
 
@@ -111,7 +83,7 @@ Requires Python 3.10+ and Git. For an agent-ready CodeGraph with no model or API
 key, install the graph and MCP extras and run one command:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.1"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -122,17 +94,40 @@ Run `codenib codegraph status /path/to/repository` to diagnose the complete
 path or `codenib codegraph uninstall /path/to/repository` to remove only the
 managed client registrations. The index remains reusable.
 
+Repositories can persist exact root-relative subtree exclusions when generated
+or vendored content should not be indexed:
+
+```bash
+codenib codegraph init /path/to/repository \
+  --exclude-dir ios/Pods \
+  --exclude-dir generated/api
+```
+
+Paths use repository-relative POSIX spelling (`/`) and name exact subtrees,
+not globs. Repeat `--exclude-dir` to replace the complete custom exclusion set. Later
+`init` and `index` runs reuse that policy from the manifest; use
+`--clear-exclude-dirs` to return to the default source surface. CodeNib does not
+implicitly treat `.gitignore` as an indexing policy, because tracked and local
+ignored source can still be intentional input.
+
+Zoekt supports the default source policy only when its fixed commit tree
+exactly matches the authenticated checkout and contains no tracked path that
+the default policy excludes. It does not currently support a non-empty custom
+exclusion set. A command that explicitly requests the `zoekt` view, including
+`--preset full`, fails closed when either condition is unmet; use the
+CodeGraph, `fast`, or semantic paths instead. Authenticated MCP serving for
+Zoekt currently requires Linux `/proc`; see the
+[source-surface boundaries](https://docs.codenib.ai/codegraph/#select-the-repository-source-surface).
+
 For a browser Wiki with hybrid BM25+dense retrieval, install the semantic extra:
 
 ```bash
-python -m pip install "codenib[semantic]==0.2.1"
+python -m pip install "codenib[semantic]"
 codenib wiki /path/to/repository
 ```
 
 Both paths keep reusable state under `~/.codenib/repositories` and leave the
-target checkout unchanged. Set `CODENIB_HOME` to relocate state. The
-[0.2.1 release notes](https://docs.codenib.ai/releases/0.2.1/) record the
-upgrade boundary and installed-product evidence.
+target checkout unchanged. Set `CODENIB_HOME` to relocate state.
 
 Preview the CodeGraph operations without installing, indexing, or configuring
 an agent:
@@ -146,7 +141,7 @@ only their package-level providers; operating-system and project prerequisites
 remain explicit:
 
 ```bash
-python -m pip install "codenib[graph]==0.2.1"
+python -m pip install "codenib[graph]"
 codenib toolchain install /path/to/repository --scope graph
 codenib doctor /path/to/repository --require graph
 ```
@@ -164,7 +159,7 @@ provider credential; interactive Ask and runtime graph exploration remain on
 the local or MCP serving path.
 
 For a repository-hosted Wiki, CodeNib also ships a reusable GitHub workflow
-that incrementally builds the same manifest, deploys the static site to Pages,
+that builds or reuses the same manifest, deploys the static site to Pages,
 and uploads the matching commit-addressed context artifact. Its default
 `semantic` route builds BM25 and vector views with a cached local Hugging Face
 model and needs no API key. An explicit `fast` route avoids the model download;
@@ -188,7 +183,7 @@ The recommended path configures installed Codex and Claude Code clients through
 their native CLIs:
 
 ```bash
-python -m pip install "codenib[graph,mcp]==0.2.1"
+python -m pip install "codenib[graph,mcp]"
 codenib codegraph init /path/to/repository
 ```
 
@@ -218,7 +213,7 @@ capabilities, loaded views, fusion, graph, and reranking trace.
 
 | Surface | Purpose |
 |---|---|
-| Incremental compiler | Build independently managed views, reuse unchanged content, repair supported transitions, and conservatively rebuild outside those boundaries |
+| View compiler | Build independently managed views, reuse current generations, and atomically rebuild changed views under one source identity |
 | Agent context runtime | Plan capability-aware retrieval and navigation, then assemble bounded source-linked evidence |
 | Retrieval | BM25, dense-vector, regex/trigram, Zoekt, fusion, and reranking paths; see the [validated model matrix](https://docs.codenib.ai/rag_ops/#validated-models) |
 | Structural context | SCIP/LSP-backed symbol graphs with source locations and typed edges |
@@ -267,8 +262,8 @@ running the credential- or toolchain-dependent tiers.
 
 ## Status
 
-CodeNib `0.1.0` is a developer preview. The CLI and manifest format are usable,
-but public interfaces may still change before a stable release. Historical
+CodeNib is currently in beta. The CLI and manifest format are usable, but
+public interfaces may still change before a stable release. Historical
 research artifacts retain their published dataset identifiers; the maintained
 package, import namespace, commands, and repository use `CodeNib`. See
 [Naming](https://docs.codenib.ai/branding/).
@@ -294,6 +289,8 @@ If you use CodeNib in your research, please cite our
 
 [Website](https://codenib.ai)
 &nbsp;&middot;&nbsp;
+[Releases](https://github.com/sysevol-ai/CodeNib/releases)
+&nbsp;&middot;&nbsp;
 [Changelog](https://github.com/sysevol-ai/CodeNib/blob/main/CHANGELOG.md)
 &nbsp;&middot;&nbsp;
 [Contributing](https://github.com/sysevol-ai/CodeNib/blob/main/CONTRIBUTING.md)

{codenib-0.2.1 → codenib-0.2.3}/codenib/__init__.py

@@ -16,6 +16,8 @@ from ._lazy import exported_dir, load_export
 from ._version import __version__
 
 if TYPE_CHECKING:  # pragma: no cover - imported only by static analyzers
+    from codenib._captured_directory import PublishedWorkspaceReceiptOwner
+    from codenib._local_workspace_provider import LocalWorkspaceProvider
     from codenib.agent.extract_agent import KeywordExtractor
     from codenib.agent.rerank_agent import RerankAgent
     from codenib.code_chunker import CodeChunker, RepoChunkingConfig
@@ -30,6 +32,14 @@ if TYPE_CHECKING:  # pragma: no cover - imported only by static analyzers
     from codenib.search import CodeSearchEngine
 
 _EXPORTS = {
+    "PublishedWorkspaceReceiptOwner": (
+        "codenib._captured_directory",
+        "PublishedWorkspaceReceiptOwner",
+    ),
+    "LocalWorkspaceProvider": (
+        "codenib._local_workspace_provider",
+        "LocalWorkspaceProvider",
+    ),
     "LSIndexer": ("codenib.ls_router", "LSIndexer"),
     "CodeGraph": ("codenib.graph.code_graph", "CodeGraph"),
     "BM25CodeIndexer": (
@@ -54,6 +64,8 @@ _EXPORTS = {
 
 __all__ = [
     "__version__",
+    "PublishedWorkspaceReceiptOwner",
+    "LocalWorkspaceProvider",
     "LSIndexer",
     "CodeGraph",
     "BM25CodeIndexer",