Feature/clarity updates 5

.gitignore

@@ -89,3 +89,5 @@ gitgalaxy/tools/supply_chain_security/README supply_chain.md
 gitgalaxy/tools/terabyte_log_scanning/README terabyte.md
 *.sqlite
 *.db
+LM-Notebook files.md
+terminology_updates.md

gitgalaxy/README.md

@@ -6,66 +6,69 @@
 
 Welcome to the internal source code for the **GitGalaxy Core Engine**. 
 
-This directory contains the central orchestrator—**GalaxyScope**—alongside the core physics, optical routing, and mathematical heuristics that power the entire system. If you are a developer looking to contribute, understand the pipeline, or run the primary CLI, here is your architectural map.
+This directory contains the central orchestrator—**GalaxyScope**—alongside the core structural mechanics, lexical routing, and mathematical heuristics that power the entire DevSecOps ecosystem. If you are a developer looking to contribute, understand the data pipeline, or run the primary CLI, here is your architectural map.
 
 ### 🗺️ The Developer Map (How the Pipeline Flows)
 
-When you trigger the `galaxyscope` command, the data flows through these five physical directories:
+When you trigger the `galaxyscope` command, the data flows through these physical directories:
 
-* **`/core/` (The Frontline):** The optical routing layer. Contains the [Aperture Filter](https://squid-protocol.github.io/gitgalaxy/02-03-aperture-filter/) and [The Prism](https://squid-protocol.github.io/gitgalaxy/02-07-the-prism/), which break down source code into structural signals, separating executable logic from ghost mass (comments) and inert binaries.
-* **`/physics/` (The Math):** The heuristics engine. Contains the [Signal Processor](https://squid-protocol.github.io/gitgalaxy/02-09-signal-processing/) and [Neural Auditor](https://squid-protocol.github.io/gitgalaxy/02-19-neural-auditor/), which apply GitGalaxy mathematics to score O(N) complexity, topological blast radius, and state flux without using ASTs.
-* **`/recorders/` (The Exporters):** The translation layer. Converts the internal state maps into highly relational [SQLite Databases](https://squid-protocol.github.io/gitgalaxy/02-21-record-keeper/), AI-agent JSON tickets, and the final 3D WebGPU payload.
-* **`/security/` (The Sentinel):** The zero-trust validation layer. Contains the [Security Lens](https://squid-protocol.github.io/gitgalaxy/02-06-security-lens/) responsible for intercepting embedded malware, hardcoded secrets, and logic bombs on the fly.
-* **`/tools/` (The Spokes):** The enterprise automation layer. Contains specialized controllers for CI/CD pipelines—like the [Supply Chain Firewall](https://squid-protocol.github.io/gitgalaxy/04-03-supply-chain-firewall/) and [PII Leak Hunter](https://squid-protocol.github.io/gitgalaxy/04-06-pii-leak-hunter/)—that consume the core engine's telemetry. **These specialized tools power our official [Zero-Trust DevSecOps GitHub Action](../github-action-read-me.md).**
+* **`/core/` (The Frontline):** The lexical routing layer. Contains the [Aperture Filter](https://squid-protocol.github.io/gitgalaxy/02-03-aperture-filter/) and [The Prism](https://squid-protocol.github.io/gitgalaxy/02-07-the-prism/), which break down source code into structural signals, stripping away inert binaries and separating executable logic from documentation.
+* **`/metrics/` (The Math):** The heuristic and statistical engine. Contains the [Signal Processor](https://squid-protocol.github.io/gitgalaxy/02-09-signal-processing/) and [Statistical Auditor](https://squid-protocol.github.io/gitgalaxy/02-19-neural-auditor/), which apply GitGalaxy mathematics to calculate O(N) complexity, topological blast radius, and architectural drift without requiring ASTs.
+* **`/security/` (The Threat Validator):** The security inference layer. Contains the [Security Lens](https://squid-protocol.github.io/gitgalaxy/02-06-security-lens/) responsible for identifying embedded malware signatures, autonomous AI execution vectors, and destructive execution patterns during Phase 1 ingestion.
+* **`/recorders/` (The Exporters):** The translation layer. Converts the internal state RAM maps into highly relational [SQLite Databases](https://squid-protocol.github.io/gitgalaxy/02-21-record-keeper/), intermediate JSON representation for AI agents, and the final WebGPU visualization payload.
+* **`/standards/` (The Calibration Layer):** The source of truth for the engine. Contains the polyglot lexical taxonomies and the global configuration profiles that tune the engine's strictness levels.
+* **`/tools/` (The Execution Controllers):** The enterprise automation layer. Contains specialized controllers for CI/CD pipelines—like the [Supply Chain Firewall](https://squid-protocol.github.io/gitgalaxy/04-03-supply-chain-firewall/) and [PII Leak Hunter](https://squid-protocol.github.io/gitgalaxy/04-06-pii-leak-hunter/)—that independently consume the core engine's telemetry. 
+
+*(Note: The `cobol_*_controller.py` scripts at the root level act as dedicated entry points for the Mainframe Legacy Modernization suite, bypassing standard Git orchestration to process flat mainframe directories).*
 
 ---
 
 ### ⚡ Performance Showcase: NVDA (NonVisual Desktop Access)
 
-To demonstrate the GalaxyScope orchestrator's capability on complex, cross-language system architecture, we unleashed it on **NVDA**, the open-source Windows screen reader. 
+To demonstrate the GalaxyScope orchestrator's capability on complex, cross-language system architecture, we executed it against **NVDA**, the open-source Windows screen reader. 
 
 Because NVDA relies heavily on bridging Python application logic with low-level C++ system hooks, it requires advanced polyglot dependency mapping. The blAST engine successfully parsed the mixed-language architecture, analyzing **236,754 lines of code** in just **5.59 seconds** (a velocity of 42,357 LOC/sec). 
 
-Crucially, during the import resolution phase, the Air-Gapped Dependency Radar successfully intercepted a structural naming collision (`fstream` vs `sstream`), proving the real-time typosquatting defenses are fully operational without relying on cloud APIs.
+Crucially, during the import resolution phase, the local dependency scanner successfully intercepted a structural naming collision (`fstream` vs `sstream`), proving the real-time typosquatting defenses are fully operational without relying on cloud-based CVE APIs.
 
-> **Note on False Positives:** Because `fstream` and `sstream` are both standard C++ libraries, this specific flag is a false positive. To prevent the engine from halting on trusted internal libraries, contributors can whitelist them by adding them to the global `approved_imports.json` registry (see [GitGalaxy Config](https://squid-protocol.github.io/gitgalaxy/06-01-gitgalaxy-config/)).
+> **Enterprise Calibration (Zero-Trust Enforcement):** Because `fstream` and `sstream` are both standard C++ libraries, flagging this collision demonstrates the engine's default Zero-Trust strictness. To prevent the pipeline from failing on trusted internal or standard libraries, DevSecOps teams simply add them to the `APPROVED_IMPORTS` allowlist in the [GitGalaxy Config](https://squid-protocol.github.io/gitgalaxy/06-01-gitgalaxy-config/).
 
-![NVDA Processing Demo](../../docs/wiki/assets/nvda_processing.gif)
+![NVDA Processing Demo](https://raw.githubusercontent.com/squid-protocol/gitgalaxy/main/docs/wiki/assets/nvda_processing.gif)
 
-```text
+~~~text
 [INFO] PASS_1.5: Running Air-Gapped Typosquatting & Dependency Confusion Radar...
 [CRITICAL] 🚨 TYPOSQUATTING DETECTED: 'fstream' in nvdaHelper/vbufBase/storage.cpp closely matches anchor 'sstream'!
 [WARNING] Intercepted 1 typosquatting attempts via repository baseline analysis.
 ...
 [INFO] --- MISSION_SUCCESS: 849 files mapped in 5.59s ---
 [INFO] --- ENGINE_TELEMETRY: Processed 236,754 lines of code at 42,357 LOC/s ---
-```
+~~~
 
 ---
 
 ### 🛠️ Local Development & GalaxyScope Execution
 
-If you are modifying the internal physics or optical routing, it is highly recommended to install the package in editable mode so your CLI commands instantly reflect your local code changes.
+If you are modifying the internal analysis logic or lexical routing, it is highly recommended to install the package in editable mode so your CLI commands instantly reflect your local code changes.
 
 From the **root directory** of the repository, run:
-```bash
+~~~bash
 pip install -e .
-```
+~~~
 
 **Important:** GitGalaxy contains an embedded commercial licensing guardrail. To prevent a 5-second execution delay while testing your code locally, you must export the Community Free Tier key into your development environment before running the orchestrator:
-```bash
+~~~bash
 export GITGALAXY_LICENSE_KEY="COMMUNITY_FREE_TIER"
-```
+~~~
 
 Once installed and the key is set, you can trigger the main orchestrator globally from your terminal. This command runs the full [Data Pipeline](https://squid-protocol.github.io/gitgalaxy/02-01-pipeline-overview/) and outputs the final artifact.
-```bash
+~~~bash
 galaxyscope /path/to/test/repo --debug
-```
+~~~
 
 Before submitting a Pull Request, ensure your changes do not skew the core baseline risk equations by running the test suite:
-```bash
+~~~bash
 python3 -m unittest discover tests/
-```
+~~~
 
 ---
 ### 🌌 Deep Dive into the Pipeline Architecture
@@ -74,4 +77,4 @@ To fully understand how GalaxyScope processes data, maps files, and applies risk
 * 📖 **[GalaxyScope CLI Reference](https://squid-protocol.github.io/gitgalaxy/01-02-galaxyscope-cli-reference/)** (Flags, outputs, and behaviors)
 * 📖 **[The Data Pipeline Overview](https://squid-protocol.github.io/gitgalaxy/02-01-pipeline-overview/)** (Step-by-step breakdown of the runtime)
 * 📖 **[Risk Exposures & Methodology](https://squid-protocol.github.io/gitgalaxy/08-01-methodology/)** (The math behind the heuristics)
-* 🪐 **[Return to the Main GitGalaxy Hub](https://github.com/squid-protocol/gitgalaxy)**
+* 🪐 **[Return to the Main GitGalaxy Hub](https://github.com/squid-protocol/gitgalaxy)**