add thesis depth map application

[gknapp1]

Adds a new type of simulation that produces a map of the melt pool depth as a function of XY location in a layer. Implements a 3DThesis application for the simulation type.

This is different than the existing melt_pool_geometry_part, which outputs melt pool geometry as a time series.

This pull request adds:

• thesis/depth_map_part simulation tool and template
• moving some thesis functionality to top-level myna.application.thesis module
• FileDpethMap output file type
• ComponentDepthMapPart component class
• Example for the depth_map_part simulation
• Test for the depth_map_part simulation configuration and running

The output data from the example, at a higher resolution of 25e-6 m for visual clarity, is plotted below.

[gknapp1]

/gemini review

[gemini-code-assist]

Code Review

This pull request introduces a new simulation type, depth_map_part, to calculate the melt pool depth as a function of XY location in a layer using 3DThesis, integrating new application logic, configuration, execution, and post-processing files. However, a security audit identified three critical vulnerabilities related to path traversal and arbitrary file copy. These stem from improper handling of user-supplied input from configuration files, which could allow an attacker to read or write arbitrary files on the system.

[gemini-code-assist]

A path traversal vulnerability exists in the configure_case method. The mynafile path, derived from user-controlled settings, is used to construct the case_dir path without proper sanitization. This allows an attacker to use ../ sequences to traverse the file system and perform file operations (like self.copy) outside of the intended directory, leading to arbitrary file writes and information disclosure. Additionally, the parse_mynafile_path_to_dict function assumes a specific directory structure; robust validation is needed to prevent errors and mitigate this vulnerability.