TypeError raised for project.yml with vars containing int inside string

Hi spaCy developers,

This is my first open-source contribution, so please let me know if there are things I could have done better.

## How to reproduce the behavior

Given project.yml:
```yaml
vars:
my_var: "1"
commands:
- name: "example"
script:
- "echo ${vars.my_var}"
```
When running:
```bash
python -m spacy project run example
```
Then I expect:
```bash
Running command: echo 1
1
```
However I get:
```bash
.venv/lib/python3.9/site-packages/spacy/cli/project/run.py", line 69, in
commands = {cmd["name"]: cmd for cmd in config.get("commands", [])}
TypeError: string indices must be integers
```

---

This seems to be related to the ```my_var: "1"```, notice that ```my_var: 1``` does work as expected.

I dug a little into your code and it seems the issue is coming from a conversion to string that only gets partially reverted in _utip.py:substitute_project_variables on line 194:
```python
cfg = Config().from_str(cfg.to_str(), overrides=overrides)
```
before this line cfg contains a `commands` attribute that is a list as expected. However, after this line, the `commands` attribute becomes a string (the string does contain the list) which seems like the issue. At that point, it became a bit too advanced for me 😅

---

There is a workaround (using integers directly), but it did take me a couple of hours to figure out this was the issue 😅 , so a fix or a better exception might save others quite a bit of time.

## Your Environment

- **spaCy version:** 3.1.2
- **Platform:** macOS-10.15.6-x86_64-i386-64bit
- **Python version:** 3.9.6

## Final remark

Great library, great documentation, loved the "free interactive course" hopefully you find some time to update it to 3.x some time.