Describe the bug
sys.path different when running code through coverage

To Reproduce
How can we reproduce the problem?

Run a source file through symlink.

Answer the questions below:

1. What version of Python are you using?
   3.11
2. What version of coverage.py shows the problem? The output of coverage debug sys is helpful.
   -- sys -------------------------------------------------------
   coverage_version: 7.13.5
   coverage_module: /usr/lib64/python3.11/site-packages/coverage/init.py
   core: -none-
   CTracer: available from /usr/lib64/python3.11/site-packages/coverage/tracer.cpython-311-x86_64-linux-gnu.so
   plugins.file_tracers: -none-
   plugins.configurers: -none-
   plugins.context_switchers: -none-
   configs_attempted: /home/hramrach/kbuild/.coveragerc
   /home/hramrach/kbuild/.coveragerc.toml
   /home/hramrach/kbuild/setup.cfg
   /home/hramrach/kbuild/tox.ini
   /home/hramrach/kbuild/pyproject.toml
   configs_read: -none-
   config_file: None
   config_contents: -none-
   data_file: -none-
   python: 3.11.14 (main, Feb 13 2026, 01:31:07) [GCC]
   platform: Linux-6.12.0-160000.26-rt-x86_64-with-glibc2.40
   implementation: CPython
   build: ('main', 'Feb 13 2026 01:31:07')
   gil_enabled: True
   executable: /usr/bin/python3.11
   pth_files: /usr/lib64/python3.11/site-packages/a1_coverage.pth
   def_encoding: utf-8
   fs_encoding: utf-8
   pid: 3047763
   cwd: /home/hramrach/kbuild
   path: /usr/bin
   /usr/lib64/python311.zip
   /usr/lib64/python3.11
   /usr/lib64/python3.11/lib-dynload
   /home/hramrach/.local/lib/python3.11/site-packages
   editable.kicad_footprint_generator-1.1.2.finder.path_hook
   /usr/lib64/python3.11/site-packages
   /usr/lib64/python3.11/_import_failed
   /usr/lib/python3.11/site-packages
   environment: HOME = /home/hramrach
   command_line: /usr/bin/coverage-3.11 debug sys
   time: 2026-04-17 12:17:50
3. What versions of what packages do you have installed? The output of pip freeze is helpful.
   aioesphomeapi==24.6.2
   aiohappyeyeballs==2.4.4
   aioquic==1.2.0
   ajsonrpc==1.2.0
   asgiref==3.8.1
   asteval==1.0.6
   async_interrupt==1.2.0
   bitarray==3.0.0
   bitstring==4.3.0
   blinker==1.9.0
   bottle==0.13.2
   cached-property==2.0.1
   certifi==2026.2.25
   cffi==2.0.0
   chacha20poly1305-reuseable==0.13.2
   charset-normalizer==3.4.4
   click==8.1.7
   coverage==7.13.5
   cryptography==43.0.0
   cssselect==1.2.0
   defcon==0.10.3
   dukpy==0.3
   ecdsa==0.19.0
   esphome==2024.12.2
   esphome-dashboard==20241217.1
   esptool==4.7.0
   feedparser==6.0.11
   Flask==3.1.0
   freetype-py==2.5.1
   future==1.0.0
   gflanguages==0.7.1
   glyphsets==1.0.0
   glyphsLib==6.9.5
   hatchling==1.29.0
   html5-parser==0.4.12
   icmplib==3.0.4
   idna==3.11
   ifaddr==0.2.0
   intelhex==2.3.0
   itsdangerous==2.2.0
   Jinja2==3.1.6
   kaitaistruct==0.10
   kconfiglib==13.7.1
   -e git+https://gitlab.com/kicad/libraries/kicad-footprint-generator.git@01422a10f9e5bfa8fe8ae3b9ab0ab0d75dd555c6#egg=kicad_footprint_generator
   ldap3==2.9.1
   loguru==0.7.0
   lxml==5.4.0
   lxml-html-clean==0.4.2
   MarkupSafe==3.0.2
   marshmallow==3.23.2
   mitmproxy==11.0.2
   mitmproxy_rs==0.10.7
   mobi==0.3.3
   multivolumefile==0.2.3
   mypy==1.10.0
   mypy-extensions==1.0.0
   noiseprotocol==0.3.1
   numpy-stl==3.2.0
   openstep_plist==0.4.0
   packaging==26.0
   paho-mqtt==1.6.1
   passlib==1.7.4
   pathspec==1.0.4
   pillow==10.4.0
   platformio==6.1.16
   pluggy==1.6.0
   protobuf==3.20.3
   publicsuffix2==2.20191221
   puremagic==1.27
   pyasn1==0.6.1
   pyasn1_modules==0.4.2
   pychm==0.8.6
   pycparser==2.21
   pycryptodome==3.22.0
   pyelftools==0.31
   pygit2==1.19.1
   pylsqpack==0.3.22
   pyOpenSSL==24.3.0
   pyperclip==1.9.0
   pyppmd==1.2.0
   pyserial==3.5
   python-augeas==1.2.0
   python-ldap==3.4.4
   python-utils==3.9.1
   PyYAML==6.0.2
   pyzstd==0.16.2
   reedsolo==1.7.0
   requests==2.32.5
   rpm==4.20.1
   ruamel.yaml==0.18.6
   ruamel.yaml.clib==0.2.12
   semantic-version==2.10.0
   service-identity==24.2.0
   sgmllib3k==1.0.0
   sortedcontainers==2.4.0
   starlette==0.39.2
   tabulate==0.9.0
   texttable==1.7.0
   tomli==2.4.1
   tornado==6.4.2
   trove-classifiers==2026.1.14.14
   typing_extensions==4.12.1
   tzdata==2024.2
   tzlocal==5.2
   ufoLib2==0.17.0
   unicodedata2==15.1.0
   urllib3==2.6.3
   urwid==2.6.16
   uvicorn==0.30.6
   voluptuous==0.14.2
   Werkzeug==3.1.3
   wsproto==1.2.0
   zeroconf==0.132.2
   zstandard==0.23.0
4. What code shows the problem? Give us a specific commit of a specific repo that we can check out. If you've already worked around the problem, please provide a commit before that fix.

#!/usr/bin/python3.11 -s

import sys

print(sys.path)

exit(0)

1. What commands should we run to reproduce the problem? Be specific. Include everything, even git clone, pip install, and so on. Explain like we're five!

mkdir dir1

cat >dir1/script <<EOF
#!/usr/bin/python3.11 -s

import sys

print(sys.path)

exit(0)
EOF

mkdir dir2

ln -s ../dir1/script dir2

python3.11 dir2/script
['/home/hramrach/kbuild/dir1', '/usr/lib64/python311.zip', '/usr/lib64/python3.11', '/usr/lib64/python3.11/lib-dynload', '/home/hramrach/.local/lib/python3.11/site-packages', 'editable.kicad_footprint_generator-1.1.2.finder.path_hook', '/usr/lib64/python3.11/site-packages', '/usr/lib64/python3.11/_import_failed', '/usr/lib/python3.11/site-packages']

coverage run dir2/script
['/home/hramrach/kbuild/dir2', '/usr/lib64/python311.zip', '/usr/lib64/python3.11', '/usr/lib64/python3.11/lib-dynload', '/home/hramrach/.local/lib/python3.11/site-packages', 'editable.kicad_footprint_generator-1.1.2.finder.path_hook', '/usr/lib64/python3.11/site-packages', '/usr/lib64/python3.11/_import_failed', '/usr/lib/python3.11/site-packages']

Expected behavior
sys.path is the same regardless of running through python interpreter or coverage

In particular local libraries should be imported correctly.