``cwltool --pack`` does not handle collisions correctly

## Expected Behavior
cwltool --pack https://raw.githubusercontent.com/common-workflow-language/cwl-v1.1/main/tests/conflict-wf.cwl should resolve conflicts and output an equivalent workflow to cwlpack output:

```cwl
$graph:
- baseCommand: echo
class: CommandLineTool
id: echo
inputs:
text:
inputBinding: {}
type: string
outputs:
fileout:
outputBinding: {glob: out.txt}
type: File
stdout: out.txt
- baseCommand: cat
class: CommandLineTool
id: cat
inputs:
file1:
inputBinding: {position: 1}
type: File
file2:
inputBinding: {position: 2}
type: File
outputs:
fileout:
outputBinding: {glob: out.txt}
type: File
stdout: out.txt
- class: Workflow
id: collision
inputs: {input_1: string, input_2: string}
outputs:
fileout: {outputSource: cat_step/fileout, type: File}
steps:
cat_step:
in:
file1: {source: echo_1/fileout}
file2: {source: echo_2/fileout}
out: [fileout]
run: '#cat'
echo_1:
in: {text: input_1}
out: [fileout]
run: '#echo'
echo_2:
in: {text: input_2}
out: [fileout]
run: '#echo'
cwlVersion: v1.1
```

## Actual Behavior
cwltool --pack https://raw.githubusercontent.com/common-workflow-language/cwl-v1.1/main/tests/conflict-wf.cwl swallows the workflow (without any error):

```json
{
"$graph": [
{
"id": "#main/cat",
"class": "CommandLineTool",
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 1
},
"id": "#main/cat/file1"
},
{
"type": "File",
"inputBinding": {
"position": 2
},
"id": "#main/cat/file2"
}
],
"baseCommand": "cat",
"stdout": "out.txt",
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "out.txt"
},
"id": "#main/cat/fileout"
}
]
},
{
"id": "#main/echo",
"class": "CommandLineTool",
"inputs": [
{
"type": "string",
"inputBinding": {},
"id": "#main/echo/text"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "out.txt"
},
"id": "#main/echo/fileout"
}
],
"baseCommand": "echo",
"stdout": "out.txt"
}
],
"cwlVersion": "v1.1"
}
```

## Your Environment
* cwltool version:
`3.1.20231020140206.dev3+g4337bee3.d20231105`