refactor: rename CIS to Membrane everywhere (#10)

Renamed Content Immune System (CIS) to Membrane across:
- Directory: src/qp_vault/cis/ -> src/qp_vault/membrane/
- Classes: CISPipeline -> MembranePipeline, CISStageRecord -> MembraneStageRecord, etc.
- Enums: CISStage -> MembraneStage, CISResult -> MembraneResult
- Events: CIS_SCAN -> MEMBRANE_SCAN, CIS_RELEASE -> MEMBRANE_RELEASE, CIS_FLAG -> MEMBRANE_FLAG
- Tests: test_cis*.py -> test_membrane*.py
- All comments, docstrings, and references

Zero CIS references remaining. 518 tests passing. Lint clean.

Author: bradleygauthier

src/qp_vault/__init__.py

@@ -32,11 +32,11 @@
 
 from qp_vault.enums import (
     AdversarialStatus,
-    CISResult,
-    CISStage,
     DataClassification,
     EventType,
     Lifecycle,
+    MembraneResult,
+    MembraneStage,
     MemoryLayer,
     ResourceStatus,
     ResourceType,
@@ -54,11 +54,11 @@
 )
 from qp_vault.models import (
     Chunk,
-    CISPipelineStatus,
-    CISStageRecord,
     Collection,
     ContentProvenance,
     HealthScore,
+    MembranePipelineStatus,
+    MembraneStageRecord,
     MerkleProof,
     Resource,
     SearchResult,
@@ -91,8 +91,8 @@
     "MerkleProof",
     "VaultEvent",
     "ContentProvenance",
-    "CISStageRecord",
-    "CISPipelineStatus",
+    "MembraneStageRecord",
+    "MembranePipelineStatus",
     # Enums
     "TrustTier",
     "DataClassification",
@@ -102,8 +102,8 @@
     "MemoryLayer",
     "EventType",
     "AdversarialStatus",
-    "CISStage",
-    "CISResult",
+    "MembraneStage",
+    "MembraneResult",
     "UploadMethod",
     # Protocols (for implementors)
     "StorageBackend",

src/qp_vault/cis/__init__.py

@@ -91,7 +91,7 @@ class AdversarialStatus(StrEnum):
     """Flagged by one or more Membrane stages. Multiplier: 0.3x."""
 
 
-class CISStage(StrEnum):
+class MembraneStage(StrEnum):
     """Membrane pipeline stages."""
 
     INGEST = "ingest"
@@ -119,7 +119,7 @@ class CISStage(StrEnum):
     """Stage 8: Attack Pattern Registry feedback loop."""
 
 
-class CISResult(StrEnum):
+class MembraneResult(StrEnum):
     """Result of a single Membrane stage evaluation."""
 
     PASS = "pass"  # nosec B105 — Membrane stage result, not a password
@@ -202,7 +202,7 @@ class EventType(StrEnum):
     SUPERSEDE = "supersede"
     VERIFY = "verify"
     SEARCH = "search"
-    CIS_SCAN = "cis_scan"
-    CIS_RELEASE = "cis_release"
-    CIS_FLAG = "cis_flag"
+    MEMBRANE_SCAN = "cis_scan"
+    MEMBRANE_RELEASE = "cis_release"
+    MEMBRANE_FLAG = "cis_flag"
     ADVERSARIAL_STATUS_CHANGE = "adversarial_status_change"

src/qp_vault/enums.py

@@ -0,0 +1,8 @@
+# Copyright 2026 Quantum Pipes Technologies, LLC
+# SPDX-License-Identifier: Apache-2.0
+
+"""Membrane: multi-stage content screening pipeline."""
+
+from qp_vault.membrane.pipeline import MembranePipeline
+
+__all__ = ["MembranePipeline"]

src/qp_vault/membrane/__init__.py

@@ -13,8 +13,8 @@
 import re
 from dataclasses import dataclass, field
 
-from qp_vault.enums import CISResult, CISStage
-from qp_vault.models import CISStageRecord
+from qp_vault.enums import MembraneResult, MembraneStage
+from qp_vault.models import MembraneStageRecord
 
 # Default blocklist patterns (prompt injection, jailbreak attempts, data exfiltration)
 DEFAULT_BLOCKLIST: list[str] = [
@@ -47,7 +47,7 @@ class InnateScanConfig:
 async def run_innate_scan(
     content: str,
     config: InnateScanConfig | None = None,
-) -> CISStageRecord:
+) -> MembraneStageRecord:
     """Run innate scan on content.
 
     Checks content against regex blocklist patterns.
@@ -57,7 +57,7 @@ async def run_innate_scan(
         config: Optional scan configuration.
 
     Returns:
-        CISStageRecord with PASS, FLAG, or FAIL result.
+        MembraneStageRecord with PASS, FLAG, or FAIL result.
     """
     if config is None:
         config = InnateScanConfig()
@@ -73,15 +73,15 @@ async def run_innate_scan(
             continue  # Skip malformed patterns
 
     if matches:
-        return CISStageRecord(
-            stage=CISStage.INNATE_SCAN,
-            result=CISResult.FLAG,
+        return MembraneStageRecord(
+            stage=MembraneStage.INNATE_SCAN,
+            result=MembraneResult.FLAG,
             matched_patterns=matches[:5],
             reasoning=f"Matched {len(matches)} blocklist patterns",
         )
 
-    return CISStageRecord(
-        stage=CISStage.INNATE_SCAN,
-        result=CISResult.PASS,  # nosec B105 — CIS stage result, not a password
+    return MembraneStageRecord(
+        stage=MembraneStage.INNATE_SCAN,
+        result=MembraneResult.PASS,  # nosec B105 — Membrane stage result, not a password
         reasoning=f"Checked {len(config.blocklist_patterns)} patterns, none matched",
     )

src/qp_vault/cis/innate_scan.py src/qp_vault/membrane/innate_scan.pysrc/qp_vault/cis/innate_scan.py renamed to src/qp_vault/membrane/innate_scan.py

@@ -1,9 +1,9 @@
 # Copyright 2026 Quantum Pipes Technologies, LLC
 # SPDX-License-Identifier: Apache-2.0
 
-"""CIS Pipeline: orchestrates multi-stage content screening.
+"""Membrane Pipeline: orchestrates multi-stage content screening.
 
-Runs content through the Content Immune System stages:
+Runs content through the Membrane stages:
 1. INNATE_SCAN — pattern-based detection (regex, blocklists)
 2. RELEASE — risk-proportionate gating decision
 
@@ -13,21 +13,21 @@
 
 from __future__ import annotations
 
-from qp_vault.cis.innate_scan import InnateScanConfig, run_innate_scan
-from qp_vault.cis.release_gate import evaluate_release
-from qp_vault.enums import CISResult, CISStage, ResourceStatus
-from qp_vault.models import CISPipelineStatus, CISStageRecord
+from qp_vault.enums import MembraneResult, MembraneStage, ResourceStatus
+from qp_vault.membrane.innate_scan import InnateScanConfig, run_innate_scan
+from qp_vault.membrane.release_gate import evaluate_release
+from qp_vault.models import MembranePipelineStatus, MembraneStageRecord
 
 
-class CISPipeline:
-    """Content Immune System pipeline.
+class MembranePipeline:
+    """Membrane pipeline.
 
     Screens content through multiple stages before allowing indexing.
     Content that fails screening is quarantined.
 
     Args:
         innate_config: Configuration for the innate scan stage.
-        enabled: Whether CIS screening is active. Default True.
+        enabled: Whether Membrane screening is active. Default True.
     """
 
     def __init__(
@@ -39,29 +39,29 @@ def __init__(
         self._innate_config = innate_config
         self._enabled = enabled
 
-    async def screen(self, content: str) -> CISPipelineStatus:
-        """Run content through the CIS pipeline.
+    async def screen(self, content: str) -> MembranePipelineStatus:
+        """Run content through the Membrane pipeline.
 
         Args:
             content: Text content to screen.
 
         Returns:
-            CISPipelineStatus with stage results and overall decision.
+            MembranePipelineStatus with stage results and overall decision.
         """
         if not self._enabled:
-            return CISPipelineStatus(
+            return MembranePipelineStatus(
                 stages=[
-                    CISStageRecord(
-                        stage=CISStage.RELEASE,
-                        result=CISResult.PASS,  # nosec B105
+                    MembraneStageRecord(
+                        stage=MembraneStage.RELEASE,
+                        result=MembraneResult.PASS,  # nosec B105
                         reasoning="Released: screening disabled",
                     ),
                 ],
-                overall_result=CISResult.PASS,  # nosec B105
+                overall_result=MembraneResult.PASS,  # nosec B105
                 recommended_status=ResourceStatus.INDEXED,
             )
 
-        stages: list[CISStageRecord] = []
+        stages: list[MembraneStageRecord] = []
 
         # Stage 1: Innate scan
         innate_result = await run_innate_scan(content, self._innate_config)
@@ -73,12 +73,12 @@ async def screen(self, content: str) -> CISPipelineStatus:
 
         # Determine overall result and recommended status
         overall = release_result.result
-        if overall == CISResult.FAIL or overall == CISResult.FLAG:
+        if overall == MembraneResult.FAIL or overall == MembraneResult.FLAG:
             status = ResourceStatus.QUARANTINED
         else:
             status = ResourceStatus.INDEXED
 
-        return CISPipelineStatus(
+        return MembranePipelineStatus(
             stages=stages,
             overall_result=overall,
             recommended_status=status,

src/qp_vault/cis/pipeline.py src/qp_vault/membrane/pipeline.pysrc/qp_vault/cis/pipeline.py renamed to src/qp_vault/membrane/pipeline.py

@@ -3,21 +3,21 @@
 
 """Release gate: risk-proportionate gating before indexing.
 
-Evaluates CIS stage results and decides whether content should be:
+Evaluates Membrane stage results and decides whether content should be:
 - RELEASED (indexed normally)
 - HELD (quarantined for human review)
 - REJECTED (blocked from indexing)
 """
 
 from __future__ import annotations
 
-from qp_vault.enums import CISResult, CISStage
-from qp_vault.models import CISStageRecord
+from qp_vault.enums import MembraneResult, MembraneStage
+from qp_vault.models import MembraneStageRecord
 
 
 async def evaluate_release(
-    stage_records: list[CISStageRecord],
-) -> CISStageRecord:
+    stage_records: list[MembraneStageRecord],
+) -> MembraneStageRecord:
     """Evaluate whether content should be released for indexing.
 
     Decision logic:
@@ -26,32 +26,32 @@ async def evaluate_release(
     - Otherwise: PASS (release)
 
     Args:
-        stage_records: Results from previous CIS stages.
+        stage_records: Results from previous Membrane stages.
 
     Returns:
-        CISStageRecord for the RELEASE stage.
+        MembraneStageRecord for the RELEASE stage.
     """
-    has_fail = any(r.result == CISResult.FAIL for r in stage_records)
-    has_flag = any(r.result == CISResult.FLAG for r in stage_records)
+    has_fail = any(r.result == MembraneResult.FAIL for r in stage_records)
+    has_flag = any(r.result == MembraneResult.FLAG for r in stage_records)
 
     if has_fail:
-        failed = [r.stage.value for r in stage_records if r.result == CISResult.FAIL]
-        return CISStageRecord(
-            stage=CISStage.RELEASE,
-            result=CISResult.FAIL,
+        failed = [r.stage.value for r in stage_records if r.result == MembraneResult.FAIL]
+        return MembraneStageRecord(
+            stage=MembraneStage.RELEASE,
+            result=MembraneResult.FAIL,
             reasoning=f"Rejected: {', '.join(failed)} failed",
         )
 
     if has_flag:
-        flagged = [r.stage.value for r in stage_records if r.result == CISResult.FLAG]
-        return CISStageRecord(
-            stage=CISStage.RELEASE,
-            result=CISResult.FLAG,
+        flagged = [r.stage.value for r in stage_records if r.result == MembraneResult.FLAG]
+        return MembraneStageRecord(
+            stage=MembraneStage.RELEASE,
+            result=MembraneResult.FLAG,
             reasoning=f"Quarantined: {', '.join(flagged)} flagged",
         )
 
-    return CISStageRecord(
-        stage=CISStage.RELEASE,
-        result=CISResult.PASS,  # nosec B105
+    return MembraneStageRecord(
+        stage=MembraneStage.RELEASE,
+        result=MembraneResult.PASS,  # nosec B105
         reasoning=f"Released: {len(stage_records)} stages passed",
     )

src/qp_vault/cis/release_gate.py src/qp_vault/membrane/release_gate.pysrc/qp_vault/cis/release_gate.py renamed to src/qp_vault/membrane/release_gate.py

@@ -9,11 +9,11 @@
 
 from qp_vault.enums import (
     AdversarialStatus,
-    CISResult,
-    CISStage,
     DataClassification,
     EventType,
     Lifecycle,
+    MembraneResult,
+    MembraneStage,
     MemoryLayer,
     ResourceStatus,
     ResourceType,
@@ -213,7 +213,7 @@ class ContentProvenance(BaseModel):
     created_at: datetime = Field(default_factory=_utcnow)
 
 
-class CISStageRecord(BaseModel):
+class MembraneStageRecord(BaseModel):
     """Result of a single Membrane pipeline stage evaluation.
 
     Every stage (INGEST through REMEMBER) creates one record per document.
@@ -222,8 +222,8 @@ class CISStageRecord(BaseModel):
 
     id: str = ""
     resource_id: str = ""
-    stage: CISStage = CISStage.INGEST
-    result: CISResult = CISResult.PASS
+    stage: MembraneStage = MembraneStage.INGEST
+    result: MembraneResult = MembraneResult.PASS
     risk_score: float = 0.0
     reasoning: str = ""
     matched_patterns: list[str] = Field(default_factory=list)
@@ -232,17 +232,17 @@ class CISStageRecord(BaseModel):
     created_at: datetime = Field(default_factory=_utcnow)
 
 
-class CISPipelineStatus(BaseModel):
+class MembranePipelineStatus(BaseModel):
     """Aggregate status of the Membrane pipeline for a single document."""
 
     resource_id: str = ""
-    stages: list[CISStageRecord] = Field(default_factory=list)
-    stages_completed: list[CISStage] = Field(default_factory=list)
-    stages_pending: list[CISStage] = Field(default_factory=list)
-    overall_result: CISResult = CISResult.PASS
+    stages: list[MembraneStageRecord] = Field(default_factory=list)
+    stages_completed: list[MembraneStage] = Field(default_factory=list)
+    stages_pending: list[MembraneStage] = Field(default_factory=list)
+    overall_result: MembraneResult = MembraneResult.PASS
     recommended_status: ResourceStatus = ResourceStatus.INDEXED
     aggregate_risk_score: float = 0.0
     recommended_action: str = "pending"
-    stage_results: list[CISStageRecord] = Field(default_factory=list)
+    stage_results: list[MembraneStageRecord] = Field(default_factory=list)
     started_at: datetime | None = None
     completed_at: datetime | None = None