style(tool-manager): polish PyQt6 UI and fix dark theme inconsistencies

ARCHITECTURE.md

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+# eSim Architecture & Workflows
+
+This document contains detailed flowcharts and diagrams mapping out the inner workings, simulation pipelines, and data transformations within eSim.
+
+---
+
+## 1. Standard Simulation Workflow
+
+This flowchart details the end-to-end user journey for a standard analog/digital simulation in eSim, from project creation to waveform analysis.
+
+```mermaid
+flowchart TD
+    %% Styling
+    classDef startend fill:#2ECC71,stroke:#27AE60,stroke-width:2px,color:#fff
+    classDef process fill:#3498DB,stroke:#2980B9,stroke-width:2px,color:#fff
+    classDef decision fill:#F1C40F,stroke:#F39C12,stroke-width:2px,color:#333
+    classDef io fill:#9B59B6,stroke:#8E44AD,stroke-width:2px,color:#fff
+
+    START([Start eSim Project]):::startend --> CREATE{New or Existing?}:::decision
+    CREATE -- New --> PROJ[Create Project Structure]:::process
+    CREATE -- Existing --> OPEN[Open Project Workspace]:::process
+
+    PROJ --> SCHEM[Draw Schematic in KiCad]:::process
+    OPEN --> SCHEM
+
+    SCHEM --> CHECK{Mixed Signal?}:::decision
+    CHECK -- Yes --> VHDL[Write VHDL/Verilog Models]:::process
+    VHDL --> GHDL[Compile via NGHDL/NgVeri]:::process
+    GHDL --> SYM[Generate KiCad Symbol]:::process
+    SYM --> SCHEM
+
+    CHECK -- No --> K2N[Run KiCad-to-Ngspice]:::process
+    K2N --> PARSE[Parse XML Netlist]:::process
+    PARSE --> SRC[Configure Sources & Analysis]:::process
+    SRC --> DEV[Configure Device Models]:::process
+
+    DEV --> SPICE[Generate .cir SPICE Netlist]:::io
+    SPICE --> NGSPICE[Execute Ngspice Simulation]:::process
+
+    NGSPICE --> OUT{Simulation Success?}:::decision
+    OUT -- No --> ERR[View Error Log & Debug]:::process
+    ERR --> SCHEM
+
+    OUT -- Yes --> RAW[Generate RAW Output Data]:::io
+    RAW --> PLOT[Extract Data for Plotting]:::process
+    PLOT --> MAT[Render matplotlib Waveforms]:::process
+
+    MAT --> END([Analyze Results]):::startend
+```
+
+---
+
+## 2. Mixed-Signal Simulation Flow (NGHDL)
+
+This diagram breaks down how eSim bridges digital logic (VHDL/Verilog) with analog simulation using GHDL and Ngspice code models.
+
+```mermaid
+flowchart TD
+    %% Styling
+    classDef input fill:#34495E,stroke:#2C3E50,stroke-width:2px,color:#fff
+    classDef process fill:#16A085,stroke:#1ABC9C,stroke-width:2px,color:#fff
+    classDef output fill:#8E44AD,stroke:#9B59B6,stroke-width:2px,color:#fff
+
+    VHDL([Write VHDL/Verilog Code]):::input --> UPLOAD[Upload via NGHDL/NgVeri UI]:::process
+    UPLOAD --> COMPILE[GHDL/Verilator Compiles Code to Shared Lib]:::process
+    COMPILE --> MODEL[Create Ngspice Code Model .cm]:::process
+    MODEL --> KICAD[Generate KiCad Component Symbol]:::output
+
+    KICAD --> SCHEM([Place Symbol in Schematic]):::input
+    SCHEM --> BRIDGE[ADC/DAC Bridge Insertion]:::process
+    BRIDGE --> SIM[Execute Mixed-Signal Co-Simulation]:::output
+```
+
+---
+
+## 3. KiCad-to-Ngspice Netlist Conversion
+
+A deep dive into the `Convert.py` backend pipeline, showing how KiCad's XML data is processed into an executable SPICE netlist.
+
+```mermaid
+flowchart TD
+    %% Styling
+    classDef input fill:#34495E,stroke:#2C3E50,stroke-width:2px,color:#fff
+    classDef process fill:#E67E22,stroke:#D35400,stroke-width:2px,color:#fff
+    classDef io fill:#9B59B6,stroke:#8E44AD,stroke-width:2px,color:#fff
+
+    XML([KiCad XML Netlist]):::input --> PARSE[Parse XML DOM]:::process
+    PARSE --> EXTRACT[Extract Components & Connections]:::process
+    EXTRACT --> MAP[Map Pins to Ngspice Nodes]:::process
+    MAP --> SUB[Resolve Subcircuits & Macros]:::process
+    SUB --> INJECT[Inject Device Parameters & Models]:::process
+    INJECT --> SPICE([Generate .cir SPICE Netlist]):::io
+```
+
+---
+
+## 4. Device Model Generation Pipeline
+
+Outlining how user-defined models (Diodes, BJTs, MOSFETs) are integrated via the Model Editor.
+
+```mermaid
+flowchart LR
+    %% Styling
+    classDef input fill:#2C3E50,stroke:#1A252F,stroke-width:2px,color:#fff
+    classDef process fill:#E74C3C,stroke:#C0392B,stroke-width:2px,color:#fff
+    classDef output fill:#F39C12,stroke:#E67E22,stroke-width:2px,color:#fff
+
+    UI([Model Editor UI]):::input --> VAL[Validate Parameters]:::process
+    VAL --> TEMPLATE[Inject Data into SPICE Template]:::process
+    TEMPLATE --> LIB([Save to project .lib file]):::output
+    LIB --> K2N([Attached during Netlist Conversion]):::output
+```