Thesis Manuscript:

Drafts: Different versions of the thesis drafts.
Final Version: The final, completed version of your thesis.

Research Materials:
Literature Review: Articles, papers, and books that you reference.
Notes: Your own notes and summaries of the literature and meetings.

Data:
Raw Data: Original, unprocessed machine data and images.
Processed Data: Data that has been processed or modified for analysis.
Data Description: Documentation describing the data, its source, and any preprocessing done.
Code:

Scripts: Coding scripts used for analysis, simulations, etc.
Documentation: Explanation of the code, how to run it, and what each part does.
Libraries: List of libraries and tools used along with their versions.

Analysis:
Results: Output of data analysis, like graphs, charts, etc.
Intermediate Analysis: Any preliminary analysis reports.

Mngmnt & Admin

Proposals: Project proposal and any revisions.
Meeting Minutes: Notes from meetings, including dates, attendees, and key decisions or action items.
Schedule: Timeline of your project, including past and future milestones.
Forms: Any administrative forms or documents.
Miscellaneous Documents: Other documents that don't fit into the above categories.

Presentations:

Slides: Slides for any presentations or defenses.
Posters: Any posters or visual aids created for presentations.