Add user onboarding Jupyter notebooks for BuildCompiler

[Gonza10V]

Motivation

• Provide new users with concise, hands-on guides to install, configure, and use the BuildCompiler package.
• Surface the primary entry points and stage responsibilities (index_collections, domestication, assembly_lvl1, assembly_lvl2, transformation, plating, full_build) so users can run planning-only or full-build workflows with explicit dependencies.
• Offer a lightweight, safe introduction to configuration and safety controls via BuildOptions to encourage deterministic, auditable runs.

Description

• Added five new user-facing notebooks under notebooks/: 01_install_and_setup.ipynb, 02_planning_only_quickstart.ipynb, 03_full_build_minimal.ipynb, 04_options_and_safety.ipynb, and 05_stage_by_stage_guide.ipynb that contain explanatory markdown and small example code snippets referencing the public API.
• Updated notebooks/notebooks.md to index the new guides and describe their purpose for users browsing the folder.
• Notebooks are provided as JSON notebook files with minimal, non-executing example code to avoid requiring heavy runtime dependencies.

Testing

• Validated notebook JSON structure for representative files with python -m json.tool notebooks/01_install_and_setup.ipynb, which succeeded.
• Validated notebook JSON structure for representative files with python -m json.tool notebooks/05_stage_by_stage_guide.ipynb, which succeeded.
• No runtime execution tests were run for notebook cells to avoid imposing optional runtime dependencies in this PR.

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Codex Task

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Use interpreter-targeted pip commands in notebook setup

The Option B setup sequence relies on !source .venv/bin/activate, but in Jupyter each ! invocation runs in its own subshell, so the activation does not persist to the later pip commands. Users who uncomment this cell will often install dependencies into the wrong interpreter (or global env), which can make the subsequent import check fail and undermines reproducibility. Prefer %pip in-notebook, or call !./.venv/bin/python -m pip ... directly.

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