Added fixes and improvements for multiple components

[taddeusb90]

• Added .gitignore entries for data/ projects/ provided new lines to ignore additional directories and scripts.

• Removed timeouts from execute_code(...) calls in ai_lab_repo.py removing timeout=60 and timeout=120 so that the code no longer forcibly terminates after a short period.

• Updated logging to show if self.verbose before printing certain debug statements** in literature_review**:

• New try-except block for FULL_TEXT retrieval in literature_review** if an arxiv.Client().results(...) call fails, an [ERROR] Could not retrieve paper message is included instead of throwing an unhandled exception.

• Introduced a new --file-path argument if the user’s research topic string includes {FILE}, the content of the file at --file-path is read and substituted in the prompt. This avoids shell “argument list too long” issues.

• Changed default model from "gpt-4" to "o1-mini" and raised the default max_context_tokens to 128000 for expanded context capacity.

• Added a new subprocess-based code execution method using psutil to distinguish busy vs. idle states. Now, if the code is continuously active (CPU usage above a small threshold), it can run longer, but will be terminated early if idle for too long or if it exceeds a hard overall runtime.