Theme re-written when saving in freshly-opened project with no open files

[wjt]

Steps to reproduce:

1. Open project
2. Close all open scenes & script files
3. Reload project
4. Close default scene
5. Monitor the filesystem for changes (e.g. watchman-wait -m 0 *)
6. Press Ctrl+S to save

Expected results:

• No files outside .godot are rewritten.

Actual result:

scenes/ui_elements/components/theme.tres-FRikAt
scenes/ui_elements/components/theme.tres
scenes/ui_elements/components

(The file with a 6-char random suffix is a temporary file used for the "save to temporary file then replace original file with rename()" pattern to atomically write to a file.)

The theme does not actually have any changes: git diff is (for me) clean after doing this.

XP Summary (total 825)

Subdomain	Skill	XP
Engineering: Optimization & Performance	Problem Solving	150
Engineering: Optimization & Performance	Creativity & Design Thinking	150
Engineering: Optimization & Performance	Technical Literacy	150
Engineering: Gameplay & Systems Programming	Problem Solving	150
Engineering: Gameplay & Systems Programming	Creativity & Design Thinking	75
Engineering: Gameplay & Systems Programming	Technical Literacy	150

[wjt]

From #1827 which I have just split into two:

@felixwalberg reports that he sees changes in those first 5 files when opening & saving the project:

@felixwalberg can you paste here the diff there?

And you said:

One thing I am noticing with running the project is that Godot can't find a bunch of UID resource paths for some of the scripts,
ex: preload("uid://c1beocky1qjxi")

Can you give more details, i.e. precise steps to reproduce and exact error?

[wjt]

Surprisingly this is actually related to #1832.

The issue there turned out to be that the pause overlay, which is an autoloaded scene so is initialised very early in the project setup, transitively depends on the credits resources, via preload()ing the title screen scene.

With that fixed in #1833, plus the change in #1828, the only file rewritten when saving a freshly-opened project with no open scenes and scripts is scenes/ui_elements/components/theme.tres. I remain interested in this problem…

[wjt]

I tried moving the default theme to the project settings and removing explicit references from all scenes in the project. (Arguably we should do that anyway!) But the behaviour remained.

I've expended enough time on this. It is harmless so I will stop here and leave this in the backlog.

[wjt]

I've tagged this with extremely high XP because I think this will need deep knowledge of the internals of Godot to solve.

My current best idea is to build Godot from source with debug symbols enabled; record a trace of the problem with https://rr-project.org/; replay the trace; set a breakpoint in the codepath that actually writes the file; identify the pointer address of the resource being saved; then set a breakpoint on that object's set_edited method and replay the trace.