Refactor/update readme conda

[Androidbeingx]

PR: README refactor, repo structure cleanup and installation documentation

Summary

This PR improves the repository documentation and tidies up the root directory structure by organising installation-related files and archiving legacy scripts. No changes to the core Python package logic.

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Changes

README.md — full refactor

The original README has been completely restructured and expanded:

• Added Table of Contents with anchor links
• Added Repository Structure section with a directory tree and table describing each folder
• Added Installation section covering both pip + venv and conda paths, including:
  • "Not sure which to use?" decision table
  • WSL detection guidance
  • Constraints file selection table per Python version and OS
  • Firewall workaround notes for corporate/university networks (e.g. Fortiguard)
  • Miniconda and Miniforge installation steps
  • Installation verification block
• Added Quick Start section for users who want to get running fast
• Restructured Programs Reference with clear syntax, descriptions and examples for each tool
• Restructured Output Files Reference into two tables (per-process metrics and aggregated metrics) replacing the original bullet-point list
• Added Legacy section documenting the deprecated Bash scripts and what superseded them
• Updated metrics-aggregator.py example to use the included sample-series/ data directly
• Added reference to sample_cpuinfo/ in the cpuinfo-tdp-finder.py example

installation/ — new directory

Moved all installation-related files from the repo root into a dedicated installation/ folder:

• All constraints-*.txt files (all Python versions, native Linux and WSL variants)
• requirements.txt
• dev-requirements.txt
• mypy-requirements.txt

legacy/ — new directory

Moved deprecated Bash scripts into a dedicated legacy/ folder:

• execution-metrics-collector.sh
• plotGraph.sh
• plot-metrics.sh

These scripts predate the current Python implementation and are no longer maintained. They are kept for historical reference only.

setup.py — path updates

Updated paths to reflect the new directory structure:

• requirements.txt path updated to installation/requirements.txt
• .sh script paths updated to legacy/execution-metrics-collector.sh, legacy/plotGraph.sh, legacy/plot-metrics.sh

MANIFEST.in — path update

Updated requirements.txt reference to installation/requirements.txt.

.gitignore — cleanup entries added

Added standard Python build artifact entries:

• *.egg-info/
• __pycache__/
• *.pyc
• build/
• dist/

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What this PR does NOT include

• No changes to the core treecript/ Python package
• No fix for the parser.py inhomogeneous array bug — this is tracked separately as a GitHub issue and will be addressed in a dedicated PR
• No offline / HPC wheel-based installation support — this is planned for a future PR pending HPC environment reconnaissance

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Testing

Tested full install from local repo using the new structure:

conda create -n Treecript python=3.10 -y
conda activate Treecript
pip install -c installation/constraints-3.10.txt .

Verified all programs run correctly after install:

• plotGraph.py ✅
• metrics-aggregator.py ✅
• tdp-finder.py ✅
• execution-metrics-collector.py ✅