[refactor] brkraw api and update for future version

[dvm-shlee]

Major Update: Redesign of Modular Architecture

This pull request implements significant architectural changes, enhancing the modularity and functionality of our codebase. Below are the key changes proposed:

API Architecture

• api.pvobj: Enhanced to parse raw data, now supports zip-compressed files through the zipfile module. Introduces PvFiles for loading individual files.
• api.analyzer: Serves as middleware to analyze datasets, ensuring compliance with current standard parsing and conversion procedures.
• api.helper: A utility module designed to fetch parameters specific to functions, such as orientation and protocol. Integrates internal parameter file processing into the data and analyzer modules.
• api.data: Acts as the backbone for file interfacing, converting raw data into Python-compatible datasets. Provides access to affine transformations, processed parameters, and converted images in numpy arrays.

Application Module

• Focuses on user interfaces like command line tools, Python interfaces, and GUIs. This update includes the tonifti app without CLI. It marks a step towards a fully featured brk-tonifti app with CLI, supporting customized conversion solutions.

Plugin and Control Updates

• api.plugin and api.ctl: Scheduled for updates in the next pull request.

Library Module Transition

• The lib module is phasing out but remains integral in this update, serving as a major interface until the new CLI is introduced.

Documentation and Contribution

• Updated contributing documents to reflect the new modular approach and the isolation of repositories that require frequent updates or active user contributions, enhancing the pull request review process and CI efficiency.

Related Issues

This pull request addresses several issues that have been identified in our application:

• Related to [Notice] Future Release Schedule and Invitation for New Maintainers #110, Sourcery refactoring suggestions #132, Bids_helper quits when method file is missing #145, Upcoming Major Update 0.4.0: Scheduled for Mid May 2024 #146, Streamlining Data Operations in Brkraw: Introducing 'PvScan' and 'PvReco' for Enhanced Raw Data Management. #155

While this update makes significant progress towards resolving these issues, complete resolution is expected in subsequent pull requests as part of ongoing improvements to our application’s architecture. This update represents a critical step towards enhancing adaptability and user experience.

@BrkRaw/Bruker