Evaluation expressions that timeout can raise JSONDecodeError

## Expected Behavior

When an evaluation expression exceeds the timeout, the resulting error should be clear that is the cause.

## Actual Behavior

At least some of the time, this situation raises a `JSONDecodeError` exception. If the user doesn't realize the timeout might be the issue, this can cause them to lose a lot of time trying to debug an issue in the expression itself where none exists.

This is sort of a sequel issue to #1680.

## Workflow Code

[eval-timeout.zip](https://github.com/common-workflow-language/cwltool/files/15297660/eval-timeout.zip)

## Full Traceback

This issue was noticed with a "real" expression that similarly built a large array of an array of files, and hit the default evaluation timeout. However, you can reproduce the issue using the attached minimal reproduction and a small evaluation timeout:

```
% venv/bin/cwltool --debug --eval-timeout=.1 wf.cwl array-in.yml
INFO venv/bin/cwltool 3.1.20240404144621
INFO Resolved 'wf.cwl' to 'file:///home/brett/Scratch/wf.cwl'
DEBUG [workflow ] initialized from file:///home/brett/Scratch/wf.cwl
INFO [workflow ] start
DEBUG [workflow ] inputs {}
INFO [workflow ] starting step build_array
DEBUG [step build_array] job input {}
DEBUG [step build_array] evaluated job input to {}
INFO [step build_array] start
Expecting value: line 1 column 1 (char 0)
script was:
01 "use strict";
02 var inputs = {};
03 var self = null;
04 var runtime = {
05 "cores": 1,
06 "ram": 256,
07 "tmpdirSize": 1024,
08 "outdirSize": 1024,
09 "tmpdir": null,
10 "outdir": null
11 };
12 (function(){
13 var result = [];
14 for (var i=0; i<100000; i++) {
15 var arr = [];
16 result.push(arr);
17 for (var j=0; j<100000; j++) {
18 var num = i * 100000 + j;
19 arr.push({
20 class: "File",
21 location: "file:///tmp/array.cwl/file" + num.toString() + ".fq",
22 format: "http://edamontology.org/format_1930"
23 });
24 }
25 }
26 return {"out_arr": result};
27 })()
stdout was: ''
stderr was: ''
Traceback (most recent call last):
File "/home/brett/Scratch/venv/lib/python3.12/site-packages/cwl_utils/sandboxjs.py", line 512, in eval
return cast(CWLOutputType, json.loads(stdout))
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

The above exception was the direct cause of the following exception:

[Note: Everything from here on is basically propagation of the same root cause exception, but here it is for completeness:]

Traceback (most recent call last):
File "/home/brett/Scratch/venv/lib/python3.12/site-packages/cwl_utils/expression.py", line 315, in do_eval
return interpolate(
^^^^^^^^^^^^
File "/home/brett/Scratch/venv/lib/python3.12/site-packages/cwl_utils/expression.py", line 215, in interpolate
e = evaluator(
^^^^^^^^^^
File "/home/brett/Scratch/venv/lib/python3.12/site-packages/cwl_utils/expression.py", line 161, in evaluator
return cast(CWLOutputType, js_engine.eval(ex, jslib, **kwargs))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/brett/Scratch/venv/lib/python3.12/site-packages/cwl_utils/sandboxjs.py", line 514, in eval
raise JavascriptException(
cwl_utils.errors.JavascriptException: Expecting value: line 1 column 1 (char 0)
script was:
01 "use strict";
02 var inputs = {};
03 var self = null;
04 var runtime = {
05 "cores": 1,
06 "ram": 256,
07 "tmpdirSize": 1024,
08 "outdirSize": 1024,
09 "tmpdir": null,
10 "outdir": null
11 };
12 (function(){
13 var result = [];
14 for (var i=0; i<100000; i++) {
15 var arr = [];
16 result.push(arr);
17 for (var j=0; j<100000; j++) {
18 var num = i * 100000 + j;
19 arr.push({
20 class: "File",
21 location: "file:///tmp/array.cwl/file" + num.toString() + ".fq",
22 format: "http://edamontology.org/format_1930"
23 });
24 }
25 }
26 return {"out_arr": result};
27 })()
stdout was: ''
stderr was: ''

ERROR Got workflow error
[error messages and tracebacks repeat from here]
```

## Your Environment
* cwltool version: 3.1.20240404144621

## Diagnosis

This occurs because of a few related issues in the way that the expression evaluation timeout is implemented:

* The evaluator stops reading expression output as soon as the timeout has been reached (i.e., the child process has been sent SIGKILL): https://github.com/common-workflow-language/cwl-utils/blob/0ad6983898f0d9001fe0f416f97c4d8b940e384a/cwl_utils/sandboxjs.py#L252
* Then it unconditionally removes the "process finished str" from the output. This is a bug because if the child process timed out, there's no reason to expect that string to be in the output, so this is just arbitrary truncation: https://github.com/common-workflow-language/cwl-utils/blob/0ad6983898f0d9001fe0f416f97c4d8b940e384a/cwl_utils/sandboxjs.py#L269-L270
* Then it polls the child process a couple times, and determines success based on this. If the child process has not actually received the SIGKILL and ended yet, it's possible `nodejs.poll()` will return `None`, causing the conditional to assume it succeeded: https://github.com/common-workflow-language/cwl-utils/blob/0ad6983898f0d9001fe0f416f97c4d8b940e384a/cwl_utils/sandboxjs.py#L272-L280

In general, there's a lot of code in `exec_js_process` that seems like it could be handled by the subprocess module directly, following the example code documented with [`Popen.communicate`](https://docs.python.org/3/library/subprocess.html#subprocess.Popen.communicate). A rough sketch would be something like:

```python
def exec_js_process(
self,
js_text: str,
timeout: float = default_timeout,
...,
) -> Tuple[int, str, str]:
...
with subprocess.Popen(
["nodejs", "--eval", js_text],
stdin=subprocess.DEVNULL,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
text=True,
encoding='utf-8',
) as nodejs:
try:
stdoutdata, stderrdata = nodejs.communicate(timeout=timeout)
except subprocess.TimeoutExpired:
nodejs.kill()
stdoutdata, stderrdata = nodejs.communicate()
returncode = -1
else:
returncode = nodejs.returncode
return returncode, stdoutdata, stderrdata
```

This would still need code at the top to find the name of the Node command, handle other arguments, etc. But I think this could replace all the process and timeout management code that currently lives in the method, while addressing the bugs above.