Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/snakemake/io/__init__.py`:
- Around line 904-908: The __str__ method of _IOFile has a broken f-string and
accesses self.file (which can raise ValueError for callable-backed IO files);
update _IOFile.__str__ to use self._file for reading the underlying path and fix
the f-string quoting/spacing logic: call is_flagged(self._file, "prepend") and
get_flag_value(self._file, "prepend") and build the returned string by
concatenating prefix + (" " if space_needed else "") + str(self._file) (or
otherwise format without nested/unescaped quotes) so the f-string syntax error
is removed and callable-backed files won't raise on stringification.

In `@src/snakemake/io/fmt.py`:
- Line 23: In fmt_iofile, using str(f.file) bypasses _IOFile.__str__ (losing
prepend(...) behavior); change the call to use str(f) (or otherwise invoke
_IOFile.__str__) so formatted IO strings go through prepend expansion—update the
expression in fmt_iofile that currently assigns f_str = str(f.file) to f_str =
str(f).

In `@tests/tests.py`:
- Around line 3136-3151: The test currently can pass when run(...) does not
raise MissingInputException and also may skip cleanup; update
test_github_issue672 to ensure an exception is expected by either using
pytest.raises(MissingInputException) around the second run(...) call or
explicitly failing if no exception is raised (e.g., call assert False or raise
AssertionError after run(...) when no exception occurs), and move the
shutil.rmtree(tmpdir, ...) cleanup into a finally block so tmpdir is always
removed; reference the test function name test_github_issue672, the run(...)
invocation and the MissingInputException class when making the changes.

---

Outside diff comments:
In `@src/snakemake/io/container.py`:
- Around line 97-103: The constructor parameter prefixes in the class __init__
now defaults to True and similarly the _plainstrings(...) call/site uses
prefixes=True, which causes CLI prefix fragments to leak outside shell contexts;
change the default for prefixes to False in the class __init__ signature and
where _plainstrings is defined/Invoked (reference the prefixes parameter and the
_plainstrings function/method) so that prepend(...) behavior remains shell-only;
update any related docstring/tests that assume the old default.

---

Nitpick comments:
In `@docs/snakefiles/rules.rst`:
- Around line 806-820: Clarify that the prepend helper affects how the shell
input placeholder is rendered by adding a sentence stating that using
prepend("--input", [...]) changes the expansion of the {input} shell placeholder
(i.e., the flag is inserted before each filename when the placeholder is
expanded), and update all inline command/keyword mentions to use literal markup
consistently (replace single-backtick instances like `--input`, `somecommand`,
`space` and `{input}` with the documentation's literal markup ``--input``,
``somecommand``, ``space`` and ``{input}``) so the wording and examples are
unambiguous.

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/snakemake/ioutils/prepend.py`:
- Around line 27-31: The ValueError in prepend.py currently references the wrong
helper name "subpath" which is misleading; update the exception message inside
the validation that raises ValueError to mention "prepend" (or the actual helper
name used) instead of "subpath" so errors accurately identify the helper, e.g.
adjust the message built around repr(path) in the block that raises ValueError
in the prepend helper/function.
- Around line 35-36: The code path that checks "if isinstance(paths,
RuleItemProxy)" always resolves the proxy as "input" by returning "lambda
wildcards, input: do(input)" which ignores RuleItemProxy.name; update this
branch to inspect the RuleItemProxy.name and return a lambda that passes the
correct rule item (e.g., input, output, params, resources) into do(...) instead
of hardcoding "input", using the proxy.name value to select the proper argument
name in the returned lambda so RuleItemProxy resolution is correct for non-input
proxies.

Verify each finding against the current code and only fix it if needed.

Duplicate comments:
In `@src/snakemake/ioutils/prepend.py`:
- Around line 27-31: The ValueError message in the prepend helper wrongly
mentions "subpath"; update the validation error in the prepend function to
reference "prepend" (or "prepend helper") so diagnostics are accurate: locate
the check in prepend that raises ValueError for non-str/non-pathlib inputs (the
block referencing variable path) and change the error string to say "Values
passed to prepend must be..." while preserving the repr(path) detail and
existing wording.
- Around line 35-37: The lambda returned from do currently hardcodes the
parameter name "input" and shadows Python's builtin; update do so that when
paths is a RuleItemProxy you return a lambda using a kwargs capture and lookup
by the proxy's name: change the lambda from "lambda wildcards, input: do(input)"
to "lambda wildcards, **kwargs: do(kwargs[paths.name])" (i.e., in the do
function, detect RuleItemProxy and resolve via paths.name from kwargs instead of
the hardcoded input identifier).

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/snakemake/ioutils/prepend.py`:
- Around line 16-22: Update the docstring in the prepend function to use the
correct parameter name: change the mention of `path_or_func` to `paths_or_func`
so it matches the actual parameter `paths_or_func` in this module (look for the
prepend function in src/snakemake/ioutils/prepend.py and update its
triple-quoted description accordingly).