Bug: temp() output files are copied to output

[kilpert]

Output files marked with temp() are copied from the local cache to the output. The expectation, however, is that those temp files are not kept.

An example Snakefile:

rule all:
    input:
        "results/b.txt"

rule a:
    output:
        temp("results/a.txt")
    shell:
        "echo a "
        ">{output} "
        "&& sleep 10 "

rule b:
    input:
        rules.a.output
    output:
        "results/b.txt"
    shell:
        "echo b "
        ">{output} "

Run completely standard (using the default 'ikim' profile):

$ snakemake
Using profile ikim for setting default command line arguments.
Assuming unrestricted shared filesystem usage.
...

The output is:

$ tree results/
results/
├── a.txt
└── b.txt

However, the output should be:

$ tree results/
results/
└── b.txt

Tested on:

$ python --version
Python 3.12.6

$ snakemake --version
8.20.4