Add formal repository structure and 30+ new files

[Devanik21]

Added a formal repository structure and 30+ new structural files without touching existing sources to avoid breaking downstream usage.

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PR created automatically by Jules for task 13368987183974811300 started by @Devanik21

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[gemini-code-assist]

Code Review

This pull request introduces the Aether-SPARC v3 framework, an asynchronous event-triggered signal processor featuring core algorithms like Adaptive Level-Crossing Sampling (ALCS), model implementations for Mamba and S4, and hardware mapping for Intel Loihi 2. The review feedback highlights several opportunities for improvement: centralizing hardcoded hardware parameters in the Loihi2Mapper, optimizing the Dockerfile for better layer caching and security, and adding error handling to shell scripts. Additionally, the reviewer recommends adopting type hints across core functions to improve maintainability and expanding the logging utility to provide a fully configured logger instance.

[gemini-code-assist]

The current order of COPY and RUN commands is inefficient for Docker layer caching. Any change in the source code will invalidate the cache and cause dependencies to be re-installed. Also, COPY . . is a poor practice as it can copy unnecessary files and potential secrets into the image, increasing its size and security risk.

I recommend the following structure to optimize caching and improve security:

# Copy only the requirements file first
COPY requirements.txt .

# Install dependencies
RUN pip install -r requirements.txt

# Then copy the application code
COPY src ./src
COPY config ./config

You should also consider adding a .dockerignore file to explicitly exclude files not needed in the image.

[gemini-code-assist]

This file only imports the logging module. To be useful as a logging utility module, it should provide a configured logger. Consider adding a function that sets up and returns a logger instance for the application to use. This centralizes logging configuration.

For example:

import logging
import sys

def get_logger(name: str) -> logging.Logger:
    logger = logging.getLogger(name)
    logger.setLevel(logging.INFO)
    handler = logging.StreamHandler(sys.stdout)
    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
    handler.setFormatter(formatter)
    logger.addHandler(handler)
    return logger