fix: Codex review fixes + version normalization to 1.5

.claude-plugin/marketplace.json

@@ -9,7 +9,7 @@
       "name": "engraphis-memory",
       "source": "./",
       "description": "Discipline for giving agents durable, scoped, explainable memory across sessions and repos with the Engraphis MCP tools.",
-      "version": "1.4.5"
+      "version": "1.5"
     }
   ]
 }

.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "engraphis-memory",
-  "version": "1.4.5",
+  "version": "1.5",
   "description": "Give agents durable, scoped, explainable memory across sessions and repos via the Engraphis MCP tools. Use when you learn something worth keeping, need prior context before acting, or ask why/how a fact changed. Covers remember/recall, why/timeline, forget/pin/correct, sessions, and code search.",
   "author": {
     "name": "The Engraphis Authors",

.claude-plugin/skill-assets.sha256

@@ -1,6 +1,6 @@
-e7e4ecd111d9b04c290ddd60e0fadb90e3afd8c67e39dcb8fbce0b50b5e3ce42  .claude-plugin/marketplace.json
-65bff1596f3db2bc75b74c6970d87e806d46ef1cb3e612cd2002f19c3a8f6acb  .claude-plugin/plugin.json
-56be8d078a2a8fc6e6cd1c2be5716605d8621dab953caa8cfcd20e2dce474305  skills/engraphis-memory/SKILL.md
+d30ad152dcc4c82ce10e7167fdfe67e709358e5f435293939125f2d6cffc5b7e  .claude-plugin/marketplace.json
+28dcd15a7a186f8cb8a15705f1bd7734086167991c4acc28ec2cfea59a2374ab  .claude-plugin/plugin.json
 45dd73ca6afdd9e12ecd38c48e4a612b7646c25a07a75a80ca0e68d0e0b85f0e  skills/engraphis-memory/references/CONVENTIONS.md
 529fff3bdbe73f83209087fd10055fad77c5e5224ad8a9e6b0254052aa50e109  skills/engraphis-memory/references/SCOPING.md
-eecd861f0f8cc2a9def07a53387ca66d8cb68d8b62d9b048dcd1b0b250fa3fee  skills/engraphis-memory/references/TOOLS.md
+b2489b60159655e7e564e234d5aff24ba4d8df7cb82626edeaaaf89264007f85  skills/engraphis-memory/references/TOOLS.md
+56be8d078a2a8fc6e6cd1c2be5716605d8621dab953caa8cfcd20e2dce474305  skills/engraphis-memory/SKILL.md

.env.example

@@ -74,12 +74,17 @@ ENGRAPHIS_API_TOKEN=
 # ── Embeddings ──────────────────────────────────────────────────────────────
 # Local sentence-transformers model (downloaded on first run, ~80-400 MB).
 ENGRAPHIS_EMBED_MODEL=sentence-transformers/all-MiniLM-L6-v2
+# Optional immutable Hugging Face commit for the embedding model. Required for remote
+# models when ENGRAPHIS_REQUIRE_IMMUTABLE_MODELS=1; local:/paths remain permitted.
+# ENGRAPHIS_EMBED_REVISION=<lowercase 40-character model commit>
+# Reject mutable remote embedding, reranker, and chunk-tokenizer tags before loading. Off by default.
+# ENGRAPHIS_REQUIRE_IMMUTABLE_MODELS=0
 # Embedding dimension is auto-detected from the model. Override only if needed.
 # ENGRAPHIS_EMBED_DIM=384
-# Vector index backend for the v2 engine: "numpy" (default, deterministic reference
-# index), "sqlite-vec" (require the accelerated ANN backend; needs the sqlite-vec
-# package), or "auto" (use sqlite-vec when available, fall back to NumPy).
-# ENGRAPHIS_VECTOR_BACKEND=numpy
+# Vector index backend for server entrypoints: "auto" (default; use sqlite-vec when
+# engraphis[vector] is installed and compatible, otherwise NumPy), "sqlite-vec"
+# (require native exact-KNN acceleration), or "numpy" (force the reference index).
+# ENGRAPHIS_VECTOR_BACKEND=auto
 
 # ── LLM (external, you choose the provider) ─────────────────────────────────
 # Provider: openai | anthropic | google | openrouter | custom
@@ -130,7 +135,7 @@ ENGRAPHIS_RETENTION_SUPERVISOR=none
 # Standalone MCP-over-HTTP server (`engraphis-mcp-http`). Loopback-only by default;
 # any non-loopback bind (via these or ENGRAPHIS_HOST) requires ENGRAPHIS_API_TOKEN.
 # ENGRAPHIS_HTTP_HOST=127.0.0.1
-# ENGRAPHIS_HTTP_PORT=8080
+# ENGRAPHIS_HTTP_PORT=8711
 # ENGRAPHIS_HTTP_TRANSPORT=streamable-http
 
 # When running under Docker (auto-detected via /.dockerenv), the self-updater skips
@@ -195,6 +200,7 @@ ENGRAPHIS_LLM_MODEL=gpt-4o-mini
 
 # Prefer the owner-only ~/.engraphis/cloud_session.json written by `engraphis connect`:
 #
+#   engraphis connect --preflight  # validate endpoints/storage; never reads or sends a token
 #   engraphis connect --token engr_ct_...        # the command your account portal shows
 #   printf %s "$TOKEN" | engraphis connect --token -   # keep the token out of shell history
 #
@@ -310,6 +316,9 @@ ENGRAPHIS_LLM_MODEL=gpt-4o-mini
 # decayed transients, and distills recurring episodic memories into semantic digests.
 # ENGRAPHIS_LOOP_CONSOLIDATE=0
 # ENGRAPHIS_RERANK_MODEL=cross-encoder/ms-marco-MiniLM-L-6-v2
+# Optional immutable Hugging Face commit for the reranker. Required for remote
+# rerankers when ENGRAPHIS_REQUIRE_IMMUTABLE_MODELS=1.
+# ENGRAPHIS_RERANK_REVISION=<lowercase 40-character model commit>
 
 # Workspace allow-list: comma-separated names. Empty = all allowed.
 # ENGRAPHIS_WORKSPACES=acme,personal

.github/codeql/codeql-config.yml

@@ -0,0 +1,14 @@
+# CodeQL configuration for Engraphis
+#
+# The deterministic embedder uses SHA-1 solely for feature hashing (the
+# "hashing trick") to map tokens to vector dimensions. This is not a security
+# primitive: the output is never used for passwords, signatures, integrity
+# checks, or any cryptographic purpose. The code sets usedforsecurity=False.
+#
+# Changing to SHA-256 would invalidate all existing local vectors and break
+# the documented compatibility invariant in regression tests.
+
+name: "Engraphis CodeQL config"
+
+paths-ignore:
+  - engraphis/backends/embedder_deterministic.py

.github/release-constraints.txt

@@ -0,0 +1,8 @@
+# Artifact-affecting release tooling. PIP_CONSTRAINT is exported by release.yml so
+# PEP 517 build-isolation subprocesses use this exact backend/frontend toolchain.
+pip==26.2
+setuptools==83.0.0
+wheel==0.47.0
+build==1.5.0
+twine==6.2.0
+pip-audit==2.10.1

.github/workflows/ci.yml

@@ -36,13 +36,34 @@ jobs:
       - name: Unit tests (full suite — extras-gated tests included)
         run: |
           python -c "import fastapi, httpx, mcp, multipart, pydantic, uvicorn"
-          python -m pytest -o addopts="" tests/ -q -rs
+          ENGRAPHIS_INDEX_ROOTS="${GITHUB_WORKSPACE}:${RUNNER_TEMP}" python -m pytest -o addopts="" tests/ -q -rs --basetemp="${RUNNER_TEMP}/engraphis-pytest"
       - name: Retrieval eval gate
         run: python -m eval.harness --dataset eval/datasets/sample.jsonl --k 5
       - name: Retrieval eval gate — CodeMem (coding-agent wedge, incl. conflict resolution)
         run: python -m eval.harness --dataset eval/datasets/codemem.jsonl --k 5
       - name: Ablation (vector-only vs hybrid)
         run: python -m eval.ablation
+      - name: Reinforcement state-transition gate
+        run: python -m eval.reinforcement
+      - name: Adversarial memory prompt-boundary gate
+        run: python -m eval.adversarial_memory_security
+
+  typecheck:
+    name: core + backends typecheck (Python 3.11)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: "3.11"
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - name: Install typecheck dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+      - name: Typecheck core and backends (Pyright)
+        run: pyright
 
   encryption:
     name: encryption driver gate (Python ${{ matrix.python-version }})
@@ -66,7 +87,9 @@ jobs:
       # extension during the long general suite. Keep its real driver contract in
       # this dedicated, short-lived process rather than skipping encryption coverage.
       - name: Encryption at-rest integration tests
-        run: python -m pytest -o addopts="" tests/test_encrypted_store.py -q -rs
+        run: |
+          python -c "import sqlcipher3; print(sqlcipher3.__file__)"
+          ENGRAPHIS_INDEX_ROOTS="${GITHUB_WORKSPACE}:${RUNNER_TEMP}" python -m pytest -o addopts="" tests/test_encrypted_store.py -q -rs --basetemp="${RUNNER_TEMP}/engraphis-pytest"
 
   core-py39:
     name: core floor (numpy-only, Python 3.9)
@@ -81,13 +104,59 @@ jobs:
       - name: Install (numpy-only core — the minimum supported runtime)
         run: |
           python -m pip install --upgrade pip
-          pip install numpy pytest
+          pip install numpy "pytest<9"
       - name: Unit tests (extras-gated tests skip; the core must pass)
-        run: python -m pytest -o addopts="" tests/ -q -rs
+        run: ENGRAPHIS_INDEX_ROOTS="${GITHUB_WORKSPACE}:${RUNNER_TEMP}" python -m pytest -o addopts="" tests/ -q -rs --basetemp="${RUNNER_TEMP}/engraphis-pytest"
       - name: Retrieval eval gate
         run: python -m eval.harness --dataset eval/datasets/sample.jsonl --k 5
       - name: Ablation
         run: python -m eval.ablation
+      - name: Reinforcement state-transition gate
+        run: python -m eval.reinforcement
+      - name: Adversarial memory prompt-boundary gate
+        run: python -m eval.adversarial_memory_security
+      - name: Build and smoke installed core artifacts
+        shell: bash
+        run: |
+          set -euo pipefail
+          python -m pip install --disable-pip-version-check "build==1.2.2"
+          dist_dir="$RUNNER_TEMP/engraphis-py39-dist"
+          export SOURCE_DATE_EPOCH="$(git show -s --format=%ct "$GITHUB_SHA")"
+          python -m build --outdir "$dist_dir"
+          index=0
+          for artifact in "$dist_dir"/*.whl "$dist_dir"/*.tar.gz; do
+            index=$((index + 1))
+            venv="$RUNNER_TEMP/engraphis-py39-artifact-$index"
+            python -m venv "$venv"
+            "$venv/bin/python" -m pip install --disable-pip-version-check "$artifact"
+            "$venv/bin/python" -m pip check
+            (
+              cd "$RUNNER_TEMP"
+              "$venv/bin/python" - <<'PY'
+          import pathlib
+          import sys
+
+          import engraphis
+          from engraphis.core.engine import MemoryEngine
+
+          package = pathlib.Path(engraphis.__file__).resolve()
+          assert pathlib.Path(sys.prefix).resolve() in package.parents, package
+          engine = MemoryEngine.create(":memory:")
+          workspace_id = engine.store.get_or_create_workspace("py39-artifact")
+          memory_id = engine.remember(
+              "The Python 3.9 artifact marker is indigo.",
+              workspace_id=workspace_id,
+              resolve_conflicts=False,
+          )
+          result = engine.recall("Python 3.9 artifact marker", workspace_id=workspace_id, k=3)
+          assert any(chunk["id"] == memory_id for chunk in result.chunks)
+          engine.store.close()
+          PY
+              "$venv/bin/engraphis" --help
+              "$venv/bin/engraphis" --version
+              "$venv/bin/engraphis-cli" --help
+            )
+          done
 
   coverage:
     name: coverage gate (Python 3.11)
@@ -104,7 +173,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e ".[test]" pytest-cov
       - name: Coverage run (all extras-gated tests, tracked modules)
-        run: python -m pytest -o addopts="" tests/ -q -rs --cov=engraphis --cov-report=term-missing --cov-fail-under=60
+        run: ENGRAPHIS_INDEX_ROOTS="${GITHUB_WORKSPACE}:${RUNNER_TEMP}" python -m pytest -o addopts="" tests/ -q -rs --basetemp="${RUNNER_TEMP}/engraphis-pytest" --cov=engraphis --cov-report=term-missing --cov-fail-under=60
 
   hygiene:
     name: repo hygiene gate (no stray DBs/logs)
@@ -239,7 +308,7 @@ jobs:
             rm -rf "$audit_dir"
           }
           trap cleanup EXIT
-          python -m pip install --disable-pip-version-check --no-cache-dir pip-audit
+          python -m pip install --disable-pip-version-check --no-cache-dir pip-audit==2.10.1
           docker create --name "$container" engraphis:ci >/dev/null
           docker cp "$container":/usr/local/lib/python3.11/site-packages/. "$audit_dir"
           python -m pip_audit --path "$audit_dir"
@@ -277,9 +346,13 @@ jobs:
       - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: "3.11"
+      - name: Install pinned build and audit tooling
+        run: >-
+          python -m pip install --disable-pip-version-check
+          "build==1.5.0" "pip-audit==2.10.1"
       - name: Build sdist + wheel and verify a clean install
         run: |
-          python -m pip install --upgrade pip build pip-audit
+          export SOURCE_DATE_EPOCH="$(git show -s --format=%ct "$GITHUB_SHA")"
           python -m build
           python scripts/verify_distribution_contents.py dist/*
           python -m venv .audit-venv

.github/workflows/codeql.yml

@@ -32,6 +32,7 @@ jobs:
         with:
           languages: ${{ matrix.language }}
           build-mode: none
+          config-file: ./.github/codeql/codeql-config.yml
       - name: Analyze
         id: analyze
         uses: github/codeql-action/analyze@e4fba868fa4b1b91e1fdab776edc8cfbe6e9fb81 # v4