Creating manuscript in existing directory overwrites references.bib file

[MKDJr]

Bug description

When creating a new project, specifically a manuscript, in an existing directory, ., my existing references.bib file was overwritten with a new references.bib file.

Steps to reproduce

1. Create a new directory. mkdir test
2. Enter into the directory. cd test
3. Create a references file with the name "references.bib". touch references.bib
4. Add any content to the references file. echo "this will be overwritten" >> references.bib
5. Create a new quarto manuscript project. quarto create project
   A. Select manuscript.
   B. Use the current directory. .

Files for the project will be created, including a references.bib file which overwrites the previous references.bib file, if one existed.

Expected behavior

If references.bib already exists, the file created by the project creation command is instead named references_1.bib, for example.

Actual behavior

The existing references.bib file is overwritten by the file of the same name created during project instantiation.

Your environment

Quarto CLI 1.4.550 in the integrated terminal of VSCode 1.86.2, running on Windows 11 Home, version 23H2, build 22631.3155.``

Quarto check output

Quarto 1.4.550
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.69.5: `OK`
      Deno version 1.37.2: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.4.550
      Path: C:\Program Files\Quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[>] Checking LaTeX....................OK
      Tex:  (not detected)

[>] Checking basic markdown render....OK

[>] Checking Python 3 installation....OK
      Version: 3.11.3
      Path: C:/Users/alder/AppData/Local/Programs/Python/Python311/python.exe
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with py -m pip install jupyter

[>] Checking R installation...........(None)

      Unable to locate an installed version of R.
      Install R from https://cloud.r-project.org/