feat: Prepare for code modularization and cleanup

- Archive old documentation and test files to `docs/archive/` and `local_tests/`.
- Remove various temporary and old files from the project root.
- Add `nekocode-rust` analysis tool and its output files (`nekocode/`, `.nekocode_sessions/`, `analysis.json`).
- Minor updates to `apps/chip8_nyash/chip8_emulator.nyash` and `local_tests` files.

This commit cleans up the repository and sets the stage for further code modularization efforts, particularly in the `src/interpreter` and `src/parser` modules, based on recent analysis.

docs/archive/mir_25_instruction_mapping.md

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+# MIR 25-Instruction Mapping Plan
+
+## Current State: 32 Instructions → Target: 25 Instructions
+
+### Tier-0: Universal Core (8 instructions)
+1. **Const** ✅ (already exists)
+2. **BinOp** ✅ (already exists) 
+3. **Compare** ✅ (already exists)
+4. **Branch** ✅ (already exists)
+5. **Jump** ✅ (already exists)
+6. **Phi** ✅ (already exists)
+7. **Call** ✅ (already exists)
+8. **Return** ✅ (already exists)
+
+### Tier-1: Nyash Semantics (12 instructions)
+9. **NewBox** ✅ (already exists)
+10. **BoxFieldLoad** ← RENAME from Load/RefGet
+11. **BoxFieldStore** ← RENAME from Store/RefSet  
+12. **BoxCall** ✅ (already exists)
+13. **Safepoint** ✅ (already exists as separate instruction)
+14. **RefGet** → RENAME to RefGet ✅
+15. **RefSet** → RENAME to RefSet ✅
+16. **WeakNew** ✅ (already exists)
+17. **WeakLoad** ✅ (already exists)
+18. **WeakCheck** ← NEW (check weak reference validity)
+19. **Send** ← NEW (Bus communication)
+20. **Recv** ← NEW (Bus communication)
+
+### Tier-2: Implementation Assistance (5 instructions)
+21. **TailCall** ← NEW (tail call optimization)
+22. **Adopt** ← NEW (ownership transfer)
+23. **Release** ← NEW (ownership release)
+24. **MemCopy** ← NEW (optimized memory operations)
+25. **AtomicFence** ← RENAME from BarrierRead/BarrierWrite
+
+## Instructions to Remove/Consolidate (7 instructions)
+- **UnaryOp** → Merge into BinOp or eliminate
+- **Load** → Consolidate into BoxFieldLoad
+- **Store** → Consolidate into BoxFieldStore
+- **ArrayGet** → Use BoxFieldLoad with array indexing
+- **ArraySet** → Use BoxFieldStore with array indexing
+- **Cast** → Eliminate or merge into BinOp
+- **Copy** → Eliminate (optimization-specific)
+- **Debug** → Remove from MIR (keep as separate system)
+- **Print** → Use Call with print function
+- **Throw** → Use Call with exception function
+- **Catch** → Use Call with catch handler
+- **RefNew** → Eliminate (use NewBox)
+- **TypeCheck** → Use Compare with type introspection
+- **BarrierRead/BarrierWrite** → Consolidate into AtomicFence
+- **FutureNew/FutureSet/Await** → Use BoxCall with Future methods
+
+## Effect System Mapping
+
+### Current → New Effect Categories
+- **Pure**: Const, BinOp, Compare, Phi, RefGet, WeakNew, WeakLoad, WeakCheck
+- **Mut**: BoxFieldStore, RefSet, Adopt, Release, MemCopy
+- **Io**: Send, Recv, Safepoint, AtomicFence
+- **Control**: Branch, Jump, Return, TailCall
+- **Context-dependent**: Call, BoxCall
+
+## Implementation Strategy
+
+### Phase 1: Core Instruction Consolidation
+1. Rename Load → BoxFieldLoad
+2. Rename Store → BoxFieldStore
+3. Remove eliminated instructions
+4. Add missing new instructions
+
+### Phase 2: Effect System Update
+1. Update effect classification to 4 categories
+2. Update all instruction effect mappings
+3. Implement effect-based optimization rules
+
+### Phase 3: Backend Updates
+1. Update Interpreter backend
+2. Update VM backend
+3. Update WASM backend
+4. Ensure all support exactly 25 instructions
+
+### Phase 4: Verification System
+1. Implement ownership forest verification
+2. Add strong cycle detection
+3. Add weak reference safety checks
+4. Implement RefSet ownership validation