logseq-matryca-parser 1.9.0__tar.gz → 1.10.0__tar.gz

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
           persist-credentials: false
 
       - name: Install pinned uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: "3.12"
@@ -65,7 +65,7 @@ jobs:
           persist-credentials: false
 
       - name: Install pinned uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: ${{ matrix.python-version }}
@@ -93,7 +93,7 @@ jobs:
           persist-credentials: false
 
       - name: Install pinned uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: "3.12"
@@ -111,10 +111,8 @@ jobs:
           --output-file "${{ runner.temp }}/requirements-audit.txt"
 
       - name: Audit exported dependencies
-        # Temporary exception governed by docs/security/DEPENDENCY_ADVISORY_EXCEPTIONS.md.
         run: >-
           uv run pip-audit --no-deps --disable-pip
-          --ignore-vuln PYSEC-2026-3740
           -r "${{ runner.temp }}/requirements-audit.txt"
 
   package-contract:
@@ -128,7 +126,7 @@ jobs:
           persist-credentials: false
 
       - name: Install pinned uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: "3.12"

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/.github/workflows/dependency-hygiene.yml

@@ -24,7 +24,7 @@ jobs:
           persist-credentials: false
 
       - name: Install pinned uv without a shared cache
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: "3.12"

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/.github/workflows/parser-adversarial.yml

@@ -24,7 +24,7 @@ jobs:
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: "3.12"

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/.github/workflows/pypi_publish.yml

@@ -28,7 +28,7 @@ jobs:
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: ${{ matrix.python-version }}
@@ -40,9 +40,7 @@ jobs:
       - name: Audit production dependencies
         run: |
           uv export --all-extras --no-dev --no-emit-workspace -o "${{ runner.temp }}/requirements-audit.txt"
-          # Temporary exception governed by docs/security/DEPENDENCY_ADVISORY_EXCEPTIONS.md.
           uv run pip-audit --no-deps --disable-pip \
-            --ignore-vuln PYSEC-2026-3740 \
             -r "${{ runner.temp }}/requirements-audit.txt"
 
       - name: Run full quality gate
@@ -68,7 +66,7 @@ jobs:
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: "3.12"

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/.github/workflows/scorecard.yml

@@ -39,6 +39,6 @@ jobs:
           if-no-files-found: error
 
       - name: Publish findings to code scanning
-        uses: github/codeql-action/upload-sarif@db488ddef3bf6cb639b32c2e9a7c0a7ea8271d28 # v4.37.8
+        uses: github/codeql-action/upload-sarif@1c5b675653bb5c22dbe9b12b556ec555138e09fd # v4.38.1
         with:
           sarif_file: results.sarif

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/.github/workflows/workflow-analysis.yml

@@ -35,7 +35,7 @@ jobs:
           persist-credentials: false
 
       - name: Install pinned uv without a shared cache
-        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
         with:
           version: "0.11.7"
           python-version: "3.12"

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/.pre-commit-config.yaml

@@ -21,3 +21,4 @@ repos:
         - pytest>=9.0.3
         - networkx>=3.0.0
         - pyvis>=0.3.2
+        - hypothesis==6.168.1

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/AGENTS.md

@@ -17,7 +17,7 @@ backlinks, exports, visualizations, and AI chunks are derived views.
 |---|---|---|
 | **LOGOS** | Parse Logseq Markdown into a deterministic AST | `LogosParser`, `StackMachineParser` |
 | **Graph** | Load a vault, resolve pages and aliases, query nodes, inspect backlinks | `LogseqGraph` |
-| **SYNAPSE** | Export lineage-aware LangChain documents, LlamaIndex nodes, and enriched chunks | `SynapseAdapter` |
+| **SYNAPSE** | Export lineage-aware LangChain documents and enriched chunks; delegate native LlamaIndex nodes to the separate companion | `SynapseAdapter` |
 | **FORGE** | Serialize JSON, clean Markdown, Logseq pages, and Obsidian-compatible output | `ForgeExporter`, `serialize_logseq_page` |
 | **KINETIC** | Run CLI parse, export, scan, visualize, agent-read, and agent-write workflows | `matryca-parse` |
 | **LENS** | Build a compatible reference-topology visualization; planned compatible deprecation follows a later Trama UI migration | `GraphVisualizer` |
@@ -79,6 +79,12 @@ make vendor-name-check
 - Treat paths, symlinks, `file://` assets, atomic replacement, and vault
   containment as security boundaries.
 - Keep optional integrations lazy; the base parser must remain lightweight.
+- The Parser `[ai]` extra provides LangChain; `[all]` also includes the
+  visualization dependencies. Neither extra installs `llama-index-core` or
+  NLTK. Do not add them back to the Parser dependency graph; native LlamaIndex
+  nodes belong to the separately maintained companion. Its proposed
+  package name is not yet published, so do not present it as currently
+  installable until its repository and distribution are verified.
 - Add focused regression tests for behavioral changes and do not lower the
   coverage floor.
 - Do not commit local caches, generated audit data, vault contents, credentials,

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/CHANGELOG.md

@@ -7,6 +7,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.10.0] - 2026-09-27
+
+### Changed
+
+- **LlamaIndex companion boundary** — keep `SynapseAdapter.to_llamaindex_nodes()`
+  as a lazy compatibility shim while moving native node construction out of the
+  Parser distribution. The proposed companion package is not yet published;
+  `[ai]` provides LangChain, while `[all]` also includes visualization
+  dependencies. Neither extra installs LlamaIndex or NLTK.
+
+### Security
+
+- **Remove Parser's NLTK dependency chain** — exclude `llama-index-core` and
+  NLTK from Parser extras, lock, and package metadata, and remove the temporary
+  Parser audit waiver. This does not resolve the upstream NLTK advisory or set
+  the separate companion's security policy.
+
 ## [1.9.0] - 2026-09-06
 
 ### Added

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/CONTRIBUTING.md

@@ -17,7 +17,7 @@ User-facing behavior is documented in:
 - [`docs/ARCHITECTURE.md`](docs/ARCHITECTURE.md) — LOGOS, SYNAPSE, `LogseqGraph`, agents, and data flow
 - [`docs/internal/LOCAL_CODE_STUDY.md`](docs/internal/LOCAL_CODE_STUDY.md) — maintainer local code audit runbook (not for public issues/CHANGELOG)
 - [`docs/logseq_ast_primer.md`](docs/logseq_ast_primer.md) — Logseq Spatial Markdown domain rules
-- [`CHANGELOG.md`](CHANGELOG.md) — latest release **1.9.0** and **Unreleased** changes (Keep a Changelog)
+- [`CHANGELOG.md`](CHANGELOG.md) — prepared **1.10.0** release notes (not yet published); latest released version remains **1.9.0** (Keep a Changelog)
 - [`docs/RELEASE_PROCESS.md`](docs/RELEASE_PROCESS.md) — version bump, tag, and PyPI publish checklist
 - [`docs/CI_ASSURANCE.md`](docs/CI_ASSURANCE.md) — pull-request, scheduled, settings-managed, and release checks
 - [`docs/CODEQL.md`](docs/CODEQL.md) — CodeQL default setup (no custom `codeql.yml`)

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/Makefile

@@ -9,7 +9,7 @@ lint-fix:
 	uv run ruff check . --fix
 
 check:
-	uv run mypy src/ tests/ examples/ scripts/check_documentation.py scripts/check_release_contract.py scripts/check_wheel_contract.py scripts/generate_supply_chain_evidence.py scripts/update_compat_snapshots.py
+	uv run mypy src/ tests/ examples/ scripts/check_documentation.py scripts/check_release_contract.py scripts/check_vendor_free_docs.py scripts/check_wheel_contract.py scripts/generate_supply_chain_evidence.py scripts/update_compat_snapshots.py
 
 vendor-name-check:
 	bash scripts/check_vendor_free_docs.sh

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: logseq-matryca-parser
-Version: 1.9.0
+Version: 1.10.0
 Summary: The Logos Protocol: Deterministic Logseq AST parsing for Matryca.ai.
 Project-URL: Homepage, https://github.com/MarcoPorcellato/logseq-matryca-parser
 Project-URL: Repository, https://github.com/MarcoPorcellato/logseq-matryca-parser
@@ -26,10 +26,8 @@ Requires-Dist: rich>=13.7.1
 Requires-Dist: typer>=0.12.0
 Provides-Extra: ai
 Requires-Dist: langchain-core; extra == 'ai'
-Requires-Dist: llama-index-core; extra == 'ai'
 Provides-Extra: all
 Requires-Dist: langchain-core; extra == 'all'
-Requires-Dist: llama-index-core; extra == 'all'
 Requires-Dist: networkx>=3.0.0; extra == 'all'
 Requires-Dist: pyvis>=0.3.2; extra == 'all'
 Provides-Extra: viz
@@ -87,7 +85,8 @@ selected by the caller.
 ### Choose your workflow
 
 - **Parse and query:** load one page or a complete vault as a typed AST and graph.
-- **Build RAG context:** export LangChain documents, LlamaIndex nodes, or enriched chunks.
+- **Build RAG context:** export LangChain documents and enriched chunks; use
+  the separate LlamaIndex companion when available.
 - **Move knowledge:** generate JSON, clean Markdown, or an Obsidian vault.
 - **Visualize:** render an interactive reference-topology graph with the transitional,
   feature-frozen LENS adapter.
@@ -110,7 +109,16 @@ The PKM (Personal Knowledge Management) world is currently forcing users to make
 ### 🔱 The Matryca Solution: The Best of Both Worlds
 **Logseq Matryca Parser** is the ultimate bridge. It allows you to **keep your sovereign, future-proof Markdown files**, while synthesizing a **Virtual Global Graph** in RAM at runtime.
 
-It acts as the strict **File System Driver** for your LLM OS. By using a deterministic Stack-Machine to parse your outliner topology, it feeds LangChain or LlamaIndex with the exact parent-child context of every single block.
+It acts as the strict **File System Driver** for your LLM OS. A deterministic
+Stack-Machine parses outliner topology and preserves each block's parent-child
+context for LangChain and, through a separate optional companion, LlamaIndex.
+
+The Parser's `[ai]` and `[all]` extras do not install LlamaIndex. The
+`logseq-matryca-parser-llamaindex` companion is planned but not yet published
+on PyPI; until then, `SynapseAdapter.to_llamaindex_nodes()` reports that the
+companion is unavailable. The Parser lock and distributions no longer include
+`llama-index-core` or NLTK. This removes that dependency chain from Parser; it
+does not claim that the separate NLTK advisory is fixed for other consumers.
 
 *You get the reasoning power of a centralized relational database, without sacrificing the plain-text soul of your Second Brain in Logseq.*
 
@@ -183,7 +191,7 @@ Logseq Matryca Parser is a deterministic **Stack-Machine engine** that acts as t
 | :--- | :--- |
 | **Parse faithfully — LOGOS** | Deterministic AST parsing for outlines, YAML and native properties, tasks, temporal markers, references, assets, code/math/query shields, stable UUIDs, line ranges, and format-preserving round trips. |
 | **Understand the vault — Graph** | Canonical pages, aliases, backlinks, inherited properties, case-insensitive lookup, namespace resolution, fluent queries, broken-reference diagnostics, and optional per-file live reloads. |
-| **Export and integrate — SYNAPSE, FORGE, LENS** | Lineage-aware LangChain and LlamaIndex exports, context-enriched chunks, JSON and Markdown serialization, Obsidian vault generation, and interactive graph visualization. |
+| **Export and integrate — SYNAPSE, FORGE, LENS** | Lineage-aware LangChain exports and context-enriched chunks; LlamaIndex nodes through a separate companion; JSON and Markdown serialization, Obsidian vault generation, and interactive graph visualization. |
 | **Automate safely — KINETIC and agent tools** | CLI parse, scan, export, and visualization; token-efficient X-Ray reads; append-only logging; bounded AST writes; vault containment, dry-run patches, and atomic replacement. |
 
 The base parser is local-first and has zero telemetry. Optional AI, watcher, and
@@ -283,6 +291,14 @@ from logseq_matryca_parser import StackMachineParser
 strict_page = StackMachineParser(strict_refs=True).parse_page_file("page.md")
 ```
 
+`uv sync --extra ai` installs LangChain. `[all]` also installs the visualization
+dependencies. Neither extra installs LlamaIndex or NLTK. LlamaIndex export
+remains available through the `SynapseAdapter` compatibility method when the
+separate `logseq-matryca-parser-llamaindex` companion is installed. That
+companion is planned but not yet published on PyPI; see the
+[support matrix](docs/reference/CONFORMANCE_SUPPORT_MATRIX.md) for the current
+boundary. The Parser itself does not install `llama-index-core` or NLTK.
+
 ### 🤖 Agentic Write Access (Append-Only)
 
 Agents such as Hermes or OpenClaw can record structured notes into a Logseq graph **without rewriting existing pages**. The helper `logseq_agent_write` only **opens the weekly agent page in append mode** (`"a"`), writes a new bullet (journal link + optional tag links + body), and never truncates or replaces prior content—so routine logging cannot wipe blocks that already live in that file.
@@ -337,6 +353,9 @@ We welcome issues, pull requests, and constructive feedback.
 
 ## 📦 Release history
 
+Version 1.10.0 release notes are prepared, but the package has not yet been
+published to PyPI. The latest published release remains v1.9.0.
+
 Read the complete [release highlights](RELEASE_HIGHLIGHTS.md), the exhaustive
 [changelog](CHANGELOG.md), or the signed artifacts on
 [GitHub Releases](https://github.com/MarcoPorcellato/logseq-matryca-parser/releases).

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/README.md

@@ -46,7 +46,8 @@ selected by the caller.
 ### Choose your workflow
 
 - **Parse and query:** load one page or a complete vault as a typed AST and graph.
-- **Build RAG context:** export LangChain documents, LlamaIndex nodes, or enriched chunks.
+- **Build RAG context:** export LangChain documents and enriched chunks; use
+  the separate LlamaIndex companion when available.
 - **Move knowledge:** generate JSON, clean Markdown, or an Obsidian vault.
 - **Visualize:** render an interactive reference-topology graph with the transitional,
   feature-frozen LENS adapter.
@@ -69,7 +70,16 @@ The PKM (Personal Knowledge Management) world is currently forcing users to make
 ### 🔱 The Matryca Solution: The Best of Both Worlds
 **Logseq Matryca Parser** is the ultimate bridge. It allows you to **keep your sovereign, future-proof Markdown files**, while synthesizing a **Virtual Global Graph** in RAM at runtime.
 
-It acts as the strict **File System Driver** for your LLM OS. By using a deterministic Stack-Machine to parse your outliner topology, it feeds LangChain or LlamaIndex with the exact parent-child context of every single block.
+It acts as the strict **File System Driver** for your LLM OS. A deterministic
+Stack-Machine parses outliner topology and preserves each block's parent-child
+context for LangChain and, through a separate optional companion, LlamaIndex.
+
+The Parser's `[ai]` and `[all]` extras do not install LlamaIndex. The
+`logseq-matryca-parser-llamaindex` companion is planned but not yet published
+on PyPI; until then, `SynapseAdapter.to_llamaindex_nodes()` reports that the
+companion is unavailable. The Parser lock and distributions no longer include
+`llama-index-core` or NLTK. This removes that dependency chain from Parser; it
+does not claim that the separate NLTK advisory is fixed for other consumers.
 
 *You get the reasoning power of a centralized relational database, without sacrificing the plain-text soul of your Second Brain in Logseq.*
 
@@ -142,7 +152,7 @@ Logseq Matryca Parser is a deterministic **Stack-Machine engine** that acts as t
 | :--- | :--- |
 | **Parse faithfully — LOGOS** | Deterministic AST parsing for outlines, YAML and native properties, tasks, temporal markers, references, assets, code/math/query shields, stable UUIDs, line ranges, and format-preserving round trips. |
 | **Understand the vault — Graph** | Canonical pages, aliases, backlinks, inherited properties, case-insensitive lookup, namespace resolution, fluent queries, broken-reference diagnostics, and optional per-file live reloads. |
-| **Export and integrate — SYNAPSE, FORGE, LENS** | Lineage-aware LangChain and LlamaIndex exports, context-enriched chunks, JSON and Markdown serialization, Obsidian vault generation, and interactive graph visualization. |
+| **Export and integrate — SYNAPSE, FORGE, LENS** | Lineage-aware LangChain exports and context-enriched chunks; LlamaIndex nodes through a separate companion; JSON and Markdown serialization, Obsidian vault generation, and interactive graph visualization. |
 | **Automate safely — KINETIC and agent tools** | CLI parse, scan, export, and visualization; token-efficient X-Ray reads; append-only logging; bounded AST writes; vault containment, dry-run patches, and atomic replacement. |
 
 The base parser is local-first and has zero telemetry. Optional AI, watcher, and
@@ -242,6 +252,14 @@ from logseq_matryca_parser import StackMachineParser
 strict_page = StackMachineParser(strict_refs=True).parse_page_file("page.md")
 ```
 
+`uv sync --extra ai` installs LangChain. `[all]` also installs the visualization
+dependencies. Neither extra installs LlamaIndex or NLTK. LlamaIndex export
+remains available through the `SynapseAdapter` compatibility method when the
+separate `logseq-matryca-parser-llamaindex` companion is installed. That
+companion is planned but not yet published on PyPI; see the
+[support matrix](docs/reference/CONFORMANCE_SUPPORT_MATRIX.md) for the current
+boundary. The Parser itself does not install `llama-index-core` or NLTK.
+
 ### 🤖 Agentic Write Access (Append-Only)
 
 Agents such as Hermes or OpenClaw can record structured notes into a Logseq graph **without rewriting existing pages**. The helper `logseq_agent_write` only **opens the weekly agent page in append mode** (`"a"`), writes a new bullet (journal link + optional tag links + body), and never truncates or replaces prior content—so routine logging cannot wipe blocks that already live in that file.
@@ -296,6 +314,9 @@ We welcome issues, pull requests, and constructive feedback.
 
 ## 📦 Release history
 
+Version 1.10.0 release notes are prepared, but the package has not yet been
+published to PyPI. The latest published release remains v1.9.0.
+
 Read the complete [release highlights](RELEASE_HIGHLIGHTS.md), the exhaustive
 [changelog](CHANGELOG.md), or the signed artifacts on
 [GitHub Releases](https://github.com/MarcoPorcellato/logseq-matryca-parser/releases).

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/RELEASE_HIGHLIGHTS.md

@@ -7,6 +7,13 @@ published artifacts and attestations, see
 
 ## Unreleased
 
+The Parser is separating native LlamaIndex export into a companion package.
+The compatibility method remains, but the proposed companion is not yet
+published; Parser `[ai]` provides LangChain, while `[all]` also includes
+visualization dependencies. Neither extra installs LlamaIndex or NLTK. See
+the [support matrix](docs/reference/CONFORMANCE_SUPPORT_MATRIX.md) for the
+current boundary.
+
 ## v1.9.0
 
 Minor release — adds a stable in-memory graph factory and clarifies the

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/SECURITY.md

@@ -4,6 +4,9 @@
 
 Security fixes are provided **only for the latest released version** on [PyPI](https://pypi.org/project/logseq-matryca-parser/). The latest supported release is v1.9.0.
 
+Version 1.10.0 release preparation does not change this support status; it will
+do so only after publication to PyPI.
+
 | Version | Supported |
 | ------- | --------- |
 | **1.9.0** (latest released) | Yes |

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/docs/ARCHITECTURE.md

@@ -54,7 +54,8 @@ flowchart LR
     AST --> Lens[LENS Visualizer]
     
     Forge --> JSON[JSON / Markdown\nPayloads]
-    Synapse --> AI[LangChain /\nLlamaIndex Nodes]
+    Synapse --> LC[LangChain Documents]
+    Synapse -. call-time delegation .-> LI[LlamaIndex companion]
     Lens --> HTML[Interactive\n3D Graph]
 ```
 
@@ -76,7 +77,7 @@ The Matryca Parser is the **deterministic translation layer**: it reads the hier
 
 **Naive / standard RAG** routinely applies **recursive or fixed-size chunkers** to raw Markdown. For Logseq-style graphs this behaves like dropping the disk into a blender: contiguous bytes are diced by character budgets, sibling blocks are fused with unrelated parents, and indentation semantics are erased. The result is embeddings of **ambiguous fragments** disconnected from lineage — a lossy projection of structured storage into unstructured bags of text.
 
-The **Matryca (Logos) approach** rejects that erosion of structure. Implementation-wise, **`StackMachineParser` (alias `LogosParser`)** performs **O(N) deterministic parsing** using spatial indentation as the sole arbiter of parent–child linkage, yielding a rigorous **Abstract Syntax Tree (AST)** (`LogseqPage`, `LogseqNode`). **`SYNAPSE`** acts as driver-level output: adapters emit **LangChain `Document`** and **LlamaIndex `TextNode`** objects whose **metadata encodes lineage** (`parent_id`, `path`, `left_id`, graph tokens), preserving the **exact topological semantics** expected by Sovereign AI and local pipelines.
+The **Matryca (Logos) approach** rejects that erosion of structure. Implementation-wise, **`StackMachineParser` (alias `LogosParser`)** performs **O(N) deterministic parsing** using spatial indentation as the sole arbiter of parent–child linkage, yielding a rigorous **Abstract Syntax Tree (AST)** (`LogseqPage`, `LogseqNode`). **`SYNAPSE`** emits lineage-aware LangChain `Document` objects and context-enriched chunks. A separate optional companion owns native LlamaIndex `TextNode` construction and can reuse the framework-neutral lineage helpers.
 
 Together, LOGOS + SYNAPSE implement **Document-Driven Development** principles. Historical specifications and blueprints are preserved in [`/docs/design-docs/`](./design-docs/) to constrain behavior, while the runtime code enforces deterministic invariants matching those documents.
 
@@ -124,7 +125,7 @@ Person(knowledgeWorker, "Knowledge Worker", "Local operator of a sovereign Logse
 System_Boundary(matrycaEcosystem, "Matryca.ai Ecosystem") {
     Container(kinetic, "KINETIC", "Typer / Rich CLI", "CLI — global `--verbose` / `--graph` callback; export (json, markdown, langchain, langchain-enriched, obsidian), visualize, demo, graph scans, `agent-read` / `agent-write` (X-Ray + headless splice), weekly append (`append`).")
     Container(logos, "LOGOS", "Python / Pydantic", "Stack-Machine AST engine — LogseqPage and LogseqNode models.")
-    Container(synapse, "SYNAPSE", "LangChain / LlamaIndex", "Framework-native exporters with parent-child metadata.")
+    Container(synapse, "SYNAPSE", "LangChain + lazy companion bridge", "LangChain documents and a call-time delegation point for the separate LlamaIndex companion.")
     Container(lens, "LENS", "NetworkX / PyVis", "Reference-topology visualization to interactive HTML.")
 }
 
@@ -183,11 +184,12 @@ flowchart LR
     FO["Obsidian YAML + ^ anchors"]:::logos
   end
 
-  subgraph SYN["SYNAPSE — Framework-native adapters"]
+  subgraph SYN["SYNAPSE — Parser-owned adapters"]
     LC["LangChain Document visitor"]:::synapse
-    LI["LlamaIndex TextNode + NodeRelationship"]:::synapse
   end
 
+  LI["Separate LlamaIndex companion\n(planned; not yet published)"]:::sink
+
   subgraph OUT["DESTINATION — LLM OS plane"]
     VS[("Vector store / index")]:::sink
     RAG["RAG retrieval + prompt assembly"]:::sink
@@ -204,7 +206,7 @@ flowchart LR
   AST --> FJ
   AST --> FO
   AST --> LC
-  AST --> LI
+  SYN -. call-time delegation .-> LI
   AST --> NX --> PV
   LC --> VS
   LI --> VS
@@ -292,17 +294,17 @@ classDiagram
   RawMarkdown --> LogseqNode : Parsing & Extraction
 ```
 
-### 3.2 SYNAPSE — AST → LangChain / LlamaIndex with lineage injection
+### 3.2 SYNAPSE — AST → LangChain, with a separate LlamaIndex companion
 
 **SYNAPSE** (`logseq_matryca_parser.synapse`) implements **`ASTVisitor`** harnesses rather than brittle string serializers.
 
 - **LangChain.** [`LangChainVisitor`](../src/logseq_matryca_parser/synapse.py) emits one **`Document`** per node with `page_content=node.clean_text` and metadata unioning **`node.properties`** with lineage fields (`uuid`, `parent_id`, `indent_level`, `source`, **`path`** — the UUID ancestry chain — `left_id`, `refs`, `task_status`, repeater, `created_at`). The underlying **`LogseqNode`** additionally carries **`task_priority`**, **`scheduled_at`**, and **`deadline_at`** (§3.1); adapters or custom visitors can project those into metadata when feeding **downstream graph databases** or **GraphRAG** filters. This preserves **parent context** explicitly in retrieval filters and re-ranking.
 
-- **LlamaIndex.** [`LlamaIndexVisitor`](../src/logseq_matryca_parser/synapse.py) constructs **`TextNode`** instances keyed by **`id_=node.uuid`**. It wires **`NodeRelationship.PARENT`** and **`CHILD`** via **`RelatedNodeInfo`**, back-linking when the parent appears earlier in preorder traversal — encoding **topology as first-class edges** beyond flat metadata dictionaries. From **v1.3.0**, it also emits **`SOURCE`** (page-level anchor via **`page_source_node_id`**), **`NEXT`**, and **`PREVIOUS`** sibling edges for spatial traversal in vector stores.
+- **LlamaIndex.** The Parser no longer constructs `TextNode` objects or imports `llama-index-core`. `SynapseAdapter.to_llamaindex_nodes()` is a call-time compatibility shim to the separate `logseq-matryca-parser-llamaindex` companion, which is planned but not yet published on PyPI. The companion owns native node construction and the `PARENT`, `CHILD`, `SOURCE`, `NEXT`, and `PREVIOUS` relationships. It can reuse the Parser's framework-neutral `build_synapse_metadata` and `page_source_node_id` helpers.
 
-- **Vector-store metadata.** **`SynapseMetadata`** and **`build_synapse_metadata`** project **`task_priority`**, temporal epoch fields, **`source_uuid`**, and joined **`path`** / **`refs`** strings into LangChain/LlamaIndex metadata without leaking raw Python list reprs.
+- **Vector-store metadata.** **`SynapseMetadata`** and **`build_synapse_metadata`** project **`task_priority`**, temporal epoch fields, **`source_uuid`**, and joined **`path`** / **`refs`** strings into LangChain metadata without leaking raw Python list reprs; the separate companion may reuse this framework-neutral projection.
 
-Together, adapters guarantee that **embedding units align with intentional block boundaries**, not splitter accidents.
+The Parser-owned LangChain and context-enriched adapters keep **embedding units aligned with intentional block boundaries**, not splitter accidents. Native LlamaIndex behavior is owned and qualified by the separate companion.
 
 #### 3.2.1 Context-enriched RAG — `SynapseAdapter.to_context_enriched_chunks`
 
@@ -637,7 +639,7 @@ Recursive and character-budget chunkers assume **approximately flat prose**. Log
 | **Property ingestion as prose**       | `collapsed:: true`, SCHEDULED markers, drawer noise degrade embedding geometry. |
 | **UUID / reference desynchronization**| Block anchors no longer correspond to embeddings; graph-native references `((uuid))` become orphaned strings. |
 
-**Deterministic AST parsing plus SYNAPSE metadata** restores **semantic sovereignty**: each retrieval unit inherits explicit **ancestor identity** (`parent_id`, cumulative `path`) and optional graph-native LlamaIndex **edges**, enabling **topology-aware augmentation** aligned with Andrej Karpathy’s mental model — the LLM “CPU” issues reads against a hierarchical disk through a **faithful driver**, not a stochastic blender.
+**Deterministic AST parsing plus SYNAPSE metadata** restores **semantic sovereignty**: each retrieval unit inherits explicit **ancestor identity** (`parent_id`, cumulative `path`) and may carry graph-native LlamaIndex **edges through the separate companion**, enabling **topology-aware augmentation** aligned with Andrej Karpathy’s mental model — the LLM “CPU” issues reads against a hierarchical disk through a **faithful driver**, not a stochastic blender.
 
 ---
 

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/docs/CI_ASSURANCE.md

@@ -101,6 +101,11 @@ make all
 make vendor-name-check
 ```
 
+The repository policy check scans Git-tracked and non-ignored untracked files,
+including hidden paths. It uses Python's standard library and Git's NUL-delimited
+file listing; enumeration or read failures are errors, not a successful empty
+scan. `uv.lock` and the checker source are explicit exemptions.
+
 When automation files change, also run actionlint and zizmor using the pinned
 versions documented in `workflow-analysis.yml`. When packaging changes, build
 wheel and sdist, run `scripts/check_wheel_contract.py`, Twine 6.2.0, and the

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/docs/CLEAN_CODE_ARCHITECTURE.md

@@ -8,9 +8,9 @@ audience: contributors
 owner: logseq-matryca-parser
 authority: source_repository
 execution_mode: reviewed
-last_verified: 2026-09-05
-verified: 2026-09-05
-stale_after: 2027-02-26
+last_verified: 2026-09-27
+verified: 2026-09-27
+stale_after: 2027-03-26
 okf_profile: matryca_okf_inspired_quality
 okf_spec_version: null
 supersedes: null
@@ -19,7 +19,7 @@ superseded_by: null
 
 # Clean Code & Clean Architecture — Logseq Matryca Parser
 
-**Version:** documents **v1.9.0** maintainer contracts (v1 structural backlog complete; parser, graph-coherence, local-assurance, and stable snapshot-graph slices merged)
+**Version:** documents maintainer contracts refreshed for **v1.10.0** release preparation; v1.10.0 is not yet published (v1 structural backlog complete; parser, graph-coherence, local-assurance, and stable snapshot-graph slices merged)
 **Audience:** contributors and Cursor agents patching `src/logseq_matryca_parser/`  
 **Companion:** [`ARCHITECTURE.md`](ARCHITECTURE.md) (LOGOS domain contract) · [`BUG_HUNT_REPORT.md`](BUG_HUNT_REPORT.md) (audit evidence) · [`CONTRIBUTING.md`](../CONTRIBUTING.md)
 
@@ -58,7 +58,7 @@ public `plumber.*` contracts. Public APIs (`LogseqGraph`, `StackMachineParser`,
 |------|-----------|-------------------------|
 | **Entities** | `logos_core.py`, `exceptions.py` | AST shape, Pydantic invariants, typed errors |
 | **Use cases** | `logos_parser.py`, `graph.py`, `logseq_markdown.py`, `logseq_paths.py` | Parse, index, serialize, path translation — **no** CLI or optional AI/viz imports |
-| **Adapters** | `synapse.py`, `forge.py`, `agent_writer.py`, `agent_press.py`, `lens.py` | Framework projections (LangChain, LlamaIndex, Obsidian, PyVis) |
+| **Adapters** | `synapse.py`, `forge.py`, `agent_writer.py`, `agent_press.py`, `lens.py` | Parser-owned projections (LangChain, Obsidian, PyVis); LlamaIndex node construction belongs to a separate companion package |
 | **Drivers** | `kinetic.py`, `kinetic_commands.py`, `kinetic_export.py`, `__main__.py` | Operator CLI — orchestrates use cases and adapters |
 
 Parser runtime modules must not import Plumber, Trama, or Brain. Trama and Brain
@@ -204,9 +204,14 @@ compatibility decision.
 
 | Area | Responsibility |
 |------|----------------|
-| Visitors | `LangChainVisitor`, `LlamaIndexVisitor` |
+| Visitors | `LangChainVisitor` |
 | Enriched RAG | `to_context_enriched_chunks`, embed expansion via `synapse_embed` |
 
+`SynapseAdapter.to_llamaindex_nodes()` is a lazy compatibility bridge, not a
+Parser-owned framework adapter. The separate LlamaIndex companion owns native
+node construction and is not yet published; the Parser dependency graph stays
+framework-light.
+
 **OCP:** `BlockEmbedExpander` / `PageEmbedExpander` in `synapse_embed.py` — [#70](https://github.com/MarcoPorcellato/logseq-matryca-parser/issues/70) **shipped**.
 
 ---

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/docs/COOKBOOK.md

@@ -11,6 +11,22 @@ uv sync --all-extras
 
 Imports use the stable package root (`logseq_matryca_parser.__all__`). See [`ARCHITECTURE.md`](ARCHITECTURE.md) for module roles and [`logseq_ast_primer.md`](logseq_ast_primer.md) for Spatial Markdown rules.
 
+The Parser's `[ai]` extra installs LangChain; `[all]` also includes its
+visualization dependencies. Neither installs LlamaIndex or NLTK. Native
+LlamaIndex nodes are delegated by `SynapseAdapter.to_llamaindex_nodes()` to the
+separate `logseq-matryca-parser-llamaindex` companion, which is planned but not
+yet published on PyPI. The Parser lock and distributions exclude both
+`llama-index-core` and NLTK; this does not resolve the separate NLTK advisory
+for applications that install NLTK through another dependency.
+
+When published, install the companion separately with either command. Run
+`uv add` from your uv-managed consuming project, not from the Parser checkout:
+
+- `pip install logseq-matryca-parser-llamaindex`
+- `uv add logseq-matryca-parser-llamaindex`
+
+Do not use these commands before publication.
+
 ---
 
 ## Recipe 1 — Single page → LangChain documents
@@ -40,14 +56,19 @@ matryca-parse export /path/to/graph output --format langchain
 
 Requires optional `[ai]` extra (`uv sync --extra ai`).
 
-For a complete offline example that exercises the LangChain, LlamaIndex, and
-context-enriched exports—including a resolved Logseq page embed—run
+For an offline example that exercises the LangChain, LlamaIndex, and
+context-enriched exports—including a resolved Logseq page embed—install the
+companion when it is published, then run
 [`examples/run_synapse_rag.py`](../examples/run_synapse_rag.py):
 
 ```bash
 uv run python examples/run_synapse_rag.py
 ```
 
+Until then, the example's LangChain and context-enriched paths can run with
+`uv sync --extra ai`; its LlamaIndex path exits with a specific companion
+installation message.
+
 ---
 
 ## Recipe 2 — Load vault + fluent graph query

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/docs/DOCUMENTATION_SYSTEM.md

@@ -83,7 +83,7 @@ date expires.
 | [`AAIF_ALIGNMENT.md`](AAIF_ALIGNMENT.md) | Agentic-interoperability alignment and non-membership boundary |
 | [`CLEAN_CODE_ARCHITECTURE.md`](CLEAN_CODE_ARCHITECTURE.md) | Architecture rings, public graph API, and dependency rules |
 | [`REPOSITORY_STELLAR_ROADMAP_2026-08-06.md`](REPOSITORY_STELLAR_ROADMAP_2026-08-06.md) | Current evidence-backed repository roadmap |
-| [`quality/ISSUE_RECONCILIATION_2026-08-06.md`](quality/ISSUE_RECONCILIATION_2026-08-06.md) | Dated GitHub backlog evidence |
+| [`quality/OPEN_ISSUE_RECONCILIATION_2026-09-24.md`](quality/OPEN_ISSUE_RECONCILIATION_2026-09-24.md) | Current dated GitHub issue and pull-request evidence |
 | [`quality/README.md`](quality/README.md) | Quality and architecture navigation |
 | [`decisions/index.md`](decisions/index.md) | Decision registry and ADR gaps |
 | [`reference/index.md`](reference/index.md) | Provenance and ecosystem relations |
@@ -112,6 +112,8 @@ Historical audits, executed roadmaps, and superseded specifications remain in
 place as evidence. They must be clearly labeled by navigation or metadata and
 must point to their successor when one exists. Do not rewrite historical
 claims, dates, or measured counts as though they described the present.
+The August 6 issue reconciliation remains historical; its successor is the
+September 24 live issue snapshot in the maintained quality bundle.
 
 ### 3.4 Generated documentation
 

{logseq_matryca_parser-1.9.0 → logseq_matryca_parser-1.10.0}/docs/README.md

@@ -48,7 +48,7 @@ entry points.
 | [`internal/LOCAL_CODE_STUDY.md`](internal/LOCAL_CODE_STUDY.md) | Maintainers | Local code audit runbook (graph-based MCP) |
 | [`logseq_ast_primer.md`](logseq_ast_primer.md) | Parser contributors | Logseq Spatial Markdown domain rules |
 | [`GOOD_FIRST_ISSUES.md`](GOOD_FIRST_ISSUES.md) | New contributors | Curated starter tasks; Clean Architecture v1 shipped in **v1.6.0** ([#78](https://github.com/MarcoPorcellato/logseq-matryca-parser/issues/78)) |
-| [`COOKBOOK.md`](COOKBOOK.md) | Integrators | Copy-paste recipes (Synapse, graph query, watcher, agents, contributor test patterns) |
+| [`COOKBOOK.md`](COOKBOOK.md) | Integrators | Copy-paste recipes (Synapse, optional companion status, graph query, watcher, agents, contributor test patterns) |
 | [`RELEASE_PROCESS.md`](RELEASE_PROCESS.md) | Maintainers | Semver, tag, and PyPI publish checklist |
 | [`CODEQL.md`](CODEQL.md) | Maintainers | CodeQL default setup notes |
 | [`BUG_HUNT_REPORT.md`](BUG_HUNT_REPORT.md) | Maintainers, contributors | Local static analysis bug audit (Clean Architecture lens, runtime evidence) |
@@ -56,7 +56,7 @@ entry points.
 | [`REPOSITORY_GOVERNANCE_AAIF_STUDY_2026-08-19.md`](REPOSITORY_GOVERNANCE_AAIF_STUDY_2026-08-19.md) | Maintainers | GitHub governance, supply-chain, agent interoperability, and AAIF-readiness study |
 | [`LSDOC_REFERENCE_STUDY_AND_EXECUTION_PLAN_2026-08-16.md`](LSDOC_REFERENCE_STUDY_AND_EXECUTION_PLAN_2026-08-16.md) | Maintainers, parser contributors | License-safe comparative study and execution plan for semantic, complexity, and source-location assurance |
 | [`README_READABILITY_REPORT_2026-08-08.md`](README_READABILITY_REPORT_2026-08-08.md) | Maintainers | Measured human and AI README assessment with a phased simplification proposal |
-| [`quality/ISSUE_RECONCILIATION_2026-08-06.md`](quality/ISSUE_RECONCILIATION_2026-08-06.md) | Maintainers, contributors | Evidence-backed disposition of every issue open at the audit baseline |
+| [`quality/OPEN_ISSUE_RECONCILIATION_2026-09-24.md`](quality/OPEN_ISSUE_RECONCILIATION_2026-09-24.md) | Maintainers | Current disposition of all 33 live open issues and four open PRs |
 | [`decisions/index.md`](decisions/index.md) | Maintainers | Canonical decision registry, including the external-oracle boundary |
 | [`reference/index.md`](reference/index.md) | Maintainers, integrators | Provenance and Matryca ecosystem relations |
 | [`reference/DIAGNOSTICS.md`](reference/DIAGNOSTICS.md) | Integrators, contributors | Stable diagnostic codes, payload schema, path safety, CLI rendering, and escalation |
@@ -84,6 +84,7 @@ entry points.
 | [`error_log.md`](error_log.md) | Informal internal fix log |
 | [`REPOSITORY_IMPROVEMENT_STUDY_2026-07-28.md`](REPOSITORY_IMPROVEMENT_STUDY_2026-07-28.md) | Superseded audit baseline; retained for provenance |
 | [`quality/ISSUE_TRIAGE_2026-07.md`](quality/ISSUE_TRIAGE_2026-07.md) | Superseded July issue-triage baseline |
+| [`quality/ISSUE_RECONCILIATION_2026-08-06.md`](quality/ISSUE_RECONCILIATION_2026-08-06.md) | Historical August issue baseline; superseded by the September 24 ledger |
 
 ## Root-level docs