Restructure package to use src/kernelbench/ layout

Restructures the package to follow Python packaging best practices and fix namespace collision issues.

Directory Structure

Before:

KernelBench/
├── src/                    ← Package code (imported as "src")
│   ├── eval.py
│   ├── utils.py
│   ├── dataset.py
│   └── prompts/
├── scripts/
└── pyproject.toml          (name = "src")

After:

KernelBench/
├── src/                    ← Container directory (not imported)
│   └── kernelbench/        ← Actual package (imported as "kernelbench")
│       ├── eval.py
│       ├── utils.py
│       ├── dataset.py
│       └── prompts/
├── scripts/
└── pyproject.toml          (name = "kernelbench")

Changes

• Package name: src → kernelbench in pyproject.toml
• Directory structure: Moved all code from src/ to src/kernelbench/
• Imports: Updated all imports from from src.* to from kernelbench.*
• Paths: Fixed REPO_TOP_PATH calculations to account for new structure

Why

• Fixes dependency name collision when installing via uv add git+... (no more generic "src" in dependencies) - A problem @S1ro1 encountered recently while doing integeration
• Prevents namespace conflicts with other projects' src/ directories
• Follows standard Python packaging conventions (src layout)
• Makes KernelBench easier to use as a library/submodule

We use the src layout rather than flat layout as KernelBench is folder of actual problem files. So we will wrap the kernelbench core logic inside src to avoid confusion.

Migration Notes

• Install in editable mode: uv pip install -e .
• All imports now use kernelbench.* instead of src.*
• No functional changes, only structural reorganization