Regression in 2020.05.28 -- pipenv omits installation of dependencies in enclosing virtualenv if they are installed system-wide

### Issue description

Let's assume that we have some system-wide pip dependencies installed. In our scenario we are creating and activating new virtualenv which starts fresh, without any dependencies. Next we are installing all dependencies from the `Pipfile.lock` using `pipenv install --ignore-pipfile --deploy --dev`. Pipenv informs that it will use the virtualenv that has been activated in previous step:

> Courtesy Notice: Pipenv found itself running within a virtual environment, so it will automatically use that environment, instead of creating its own for any project. You can set PIPENV_IGNORE_VIRTUALENVS=1 to force pipenv to ignore that environment and create its own instead. You can set PIPENV_VERBOSITY=-1 to suppress this warning.

Once the installation is done we can see that **dependencies that were previously installed system-wide were omitted and not installed in the virtualenv**.

<details>
<summary>Pipfile</summary>

```
[[source]]
name = "pypi"
url = "https://pypi.org/simple"
verify_ssl = true

[dev-packages]
pytest = "==5.4.1"
pytest-cov = "==2.8.1"

[packages]
boto3 = "==1.12.39"
requests = "==2.23.0"
zipstream-new = "==1.1.7"

[requires]
python_version = "3.7"
```
</details>

<details>
<summary>Pipfile.lock</summary>

```
{
    "_meta": {
        "hash": {
            "sha256": "20a3bc4432a7aac37224b2fbb32564689fe917920e9b537c40db47251159121c"
        },
        "pipfile-spec": 6,
        "requires": {
            "python_version": "3.7"
        },
        "sources": [
            {
                "name": "pypi",
                "url": "https://pypi.org/simple",
                "verify_ssl": true
            }
        ]
    },
    "default": {
        "boto3": {
            "hashes": [
                "sha256:970bd7b332e73d7b51077ed36772c634811b38c81b0cc6ed0f910e50d7ebadf8",
                "sha256:cdd79a3a7bbe1f33a365f0acfcc75c4405b482b3eb9ce3f4e6b16c418e201ac3"
            ],
            "index": "pypi",
            "version": "==1.12.39"
        },
        "botocore": {
            "hashes": [
                "sha256:a474131ba7a7d700b91696a27e8cdcf1b473084addf92f90b269ebd8f5c3d3e0",
                "sha256:b805691b4dedcb2a252f52347479ff351429624a873f001b6a1c81aca03dccee"
            ],
            "version": "==1.15.49"
        },
        "certifi": {
            "hashes": [
                "sha256:1d987a998c75633c40847cc966fcf5904906c920a7f17ef374f5aa4282abd304",
                "sha256:51fcb31174be6e6664c5f69e3e1691a2d72a1a12e90f872cbdb1567eb47b6519"
            ],
            "version": "==2020.4.5.1"
        },
        "chardet": {
            "hashes": [
                "sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae",
                "sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691"
            ],
            "version": "==3.0.4"
        },
        "docutils": {
            "hashes": [
                "sha256:6c4f696463b79f1fb8ba0c594b63840ebd41f059e92b31957c46b74a4599b6d0",
                "sha256:9e4d7ecfc600058e07ba661411a2b7de2fd0fafa17d1a7f7361cd47b1175c827",
                "sha256:a2aeea129088da402665e92e0b25b04b073c04b2dce4ab65caaa38b7ce2e1a99"
            ],
            "version": "==0.15.2"
        },
        "idna": {
            "hashes": [
                "sha256:7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb",
                "sha256:a068a21ceac8a4d63dbfd964670474107f541babbd2250d61922f029858365fa"
            ],
            "version": "==2.9"
        },
        "jmespath": {
            "hashes": [
                "sha256:b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9",
                "sha256:cdf6525904cc597730141d61b36f2e4b8ecc257c420fa2f4549bac2c2d0cb72f"
            ],
            "version": "==0.10.0"
        },
        "python-dateutil": {
            "hashes": [
                "sha256:73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c",
                "sha256:75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"
            ],
            "version": "==2.8.1"
        },
        "requests": {
            "hashes": [
                "sha256:43999036bfa82904b6af1d99e4882b560e5e2c68e5c4b0aa03b655f3d7d73fee",
                "sha256:b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6"
            ],
            "index": "pypi",
            "version": "==2.23.0"
        },
        "s3transfer": {
            "hashes": [
                "sha256:2482b4259524933a022d59da830f51bd746db62f047d6eb213f2f8855dcb8a13",
                "sha256:921a37e2aefc64145e7b73d50c71bb4f26f46e4c9f414dc648c6245ff92cf7db"
            ],
            "version": "==0.3.3"
        },
        "six": {
            "hashes": [
                "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
                "sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
            ],
            "version": "==1.15.0"
        },
        "urllib3": {
            "hashes": [
                "sha256:3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527",
                "sha256:88206b0eb87e6d677d424843ac5209e3fb9d0190d0ee169599165ec25e9d9115"
            ],
            "markers": "python_version != '3.4'",
            "version": "==1.25.9"
        },
        "zipstream-new": {
            "hashes": [
                "sha256:779d47c2c47934db610f8ce25ad5bd3bee33d805fe3ea1675f50ba0b01fb6497",
                "sha256:c5708462c5a12e227b3407e46489b5ffb516c38330983f1638d6cea83e653fb1"
            ],
            "index": "pypi",
            "version": "==1.1.7"
        }
    },
    "develop": {
        "attrs": {
            "hashes": [
                "sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c",
                "sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"
            ],
            "version": "==19.3.0"
        },
        "coverage": {
            "hashes": [
                "sha256:00f1d23f4336efc3b311ed0d807feb45098fc86dee1ca13b3d6768cdab187c8a",
                "sha256:01333e1bd22c59713ba8a79f088b3955946e293114479bbfc2e37d522be03355",
                "sha256:0cb4be7e784dcdc050fc58ef05b71aa8e89b7e6636b99967fadbdba694cf2b65",
                "sha256:0e61d9803d5851849c24f78227939c701ced6704f337cad0a91e0972c51c1ee7",
                "sha256:1601e480b9b99697a570cea7ef749e88123c04b92d84cedaa01e117436b4a0a9",
                "sha256:2742c7515b9eb368718cd091bad1a1b44135cc72468c731302b3d641895b83d1",
                "sha256:2d27a3f742c98e5c6b461ee6ef7287400a1956c11421eb574d843d9ec1f772f0",
                "sha256:402e1744733df483b93abbf209283898e9f0d67470707e3c7516d84f48524f55",
                "sha256:5c542d1e62eece33c306d66fe0a5c4f7f7b3c08fecc46ead86d7916684b36d6c",
                "sha256:5f2294dbf7875b991c381e3d5af2bcc3494d836affa52b809c91697449d0eda6",
                "sha256:6402bd2fdedabbdb63a316308142597534ea8e1895f4e7d8bf7476c5e8751fef",
                "sha256:66460ab1599d3cf894bb6baee8c684788819b71a5dc1e8fa2ecc152e5d752019",
                "sha256:782caea581a6e9ff75eccda79287daefd1d2631cc09d642b6ee2d6da21fc0a4e",
                "sha256:79a3cfd6346ce6c13145731d39db47b7a7b859c0272f02cdb89a3bdcbae233a0",
                "sha256:7a5bdad4edec57b5fb8dae7d3ee58622d626fd3a0be0dfceda162a7035885ecf",
                "sha256:8fa0cbc7ecad630e5b0f4f35b0f6ad419246b02bc750de7ac66db92667996d24",
                "sha256:a027ef0492ede1e03a8054e3c37b8def89a1e3c471482e9f046906ba4f2aafd2",
                "sha256:a3f3654d5734a3ece152636aad89f58afc9213c6520062db3978239db122f03c",
                "sha256:a82b92b04a23d3c8a581fc049228bafde988abacba397d57ce95fe95e0338ab4",
                "sha256:acf3763ed01af8410fc36afea23707d4ea58ba7e86a8ee915dfb9ceff9ef69d0",
                "sha256:adeb4c5b608574a3d647011af36f7586811a2c1197c861aedb548dd2453b41cd",
                "sha256:b83835506dfc185a319031cf853fa4bb1b3974b1f913f5bb1a0f3d98bdcded04",
                "sha256:bb28a7245de68bf29f6fb199545d072d1036a1917dca17a1e75bbb919e14ee8e",
                "sha256:bf9cb9a9fd8891e7efd2d44deb24b86d647394b9705b744ff6f8261e6f29a730",
                "sha256:c317eaf5ff46a34305b202e73404f55f7389ef834b8dbf4da09b9b9b37f76dd2",
                "sha256:dbe8c6ae7534b5b024296464f387d57c13caa942f6d8e6e0346f27e509f0f768",
                "sha256:de807ae933cfb7f0c7d9d981a053772452217df2bf38e7e6267c9cbf9545a796",
                "sha256:dead2ddede4c7ba6cb3a721870f5141c97dc7d85a079edb4bd8d88c3ad5b20c7",
                "sha256:dec5202bfe6f672d4511086e125db035a52b00f1648d6407cc8e526912c0353a",
                "sha256:e1ea316102ea1e1770724db01998d1603ed921c54a86a2efcb03428d5417e489",
                "sha256:f90bfc4ad18450c80b024036eaf91e4a246ae287701aaa88eaebebf150868052"
            ],
            "version": "==5.1"
        },
        "importlib-metadata": {
            "hashes": [
                "sha256:2a688cbaa90e0cc587f1df48bdc97a6eadccdcd9c35fb3f976a09e3b5016d90f",
                "sha256:34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e"
            ],
            "markers": "python_version < '3.8'",
            "version": "==1.6.0"
        },
        "more-itertools": {
            "hashes": [
                "sha256:558bb897a2232f5e4f8e2399089e35aecb746e1f9191b6584a151647e89267be",
                "sha256:7818f596b1e87be009031c7653d01acc46ed422e6656b394b0f765ce66ed4982"
            ],
            "version": "==8.3.0"
        },
        "packaging": {
            "hashes": [
                "sha256:4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8",
                "sha256:998416ba6962ae7fbd6596850b80e17859a5753ba17c32284f67bfff33784181"
            ],
            "version": "==20.4"
        },
        "pluggy": {
            "hashes": [
                "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0",
                "sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"
            ],
            "version": "==0.13.1"
        },
        "py": {
            "hashes": [
                "sha256:5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa",
                "sha256:c20fdd83a5dbc0af9efd622bee9a5564e278f6380fffcacc43ba6f43db2813b0"
            ],
            "version": "==1.8.1"
        },
        "pyparsing": {
            "hashes": [
                "sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1",
                "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"
            ],
            "version": "==2.4.7"
        },
        "pytest": {
            "hashes": [
                "sha256:0e5b30f5cb04e887b91b1ee519fa3d89049595f428c1db76e73bd7f17b09b172",
                "sha256:84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970"
            ],
            "index": "pypi",
            "version": "==5.4.1"
        },
        "pytest-cov": {
            "hashes": [
                "sha256:cc6742d8bac45070217169f5f72ceee1e0e55b0221f54bcf24845972d3a47f2b",
                "sha256:cdbdef4f870408ebdbfeb44e63e07eb18bb4619fae852f6e760645fa36172626"
            ],
            "index": "pypi",
            "version": "==2.8.1"
        },
        "six": {
            "hashes": [
                "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
                "sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
            ],
            "version": "==1.15.0"
        },
        "wcwidth": {
            "hashes": [
                "sha256:cafe2186b3c009a04067022ce1dcd79cb38d8d65ee4f4791b8888d6599d1bbe1",
                "sha256:ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1"
            ],
            "version": "==0.1.9"
        },
        "zipp": {
            "hashes": [
                "sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
                "sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
            ],
            "version": "==3.1.0"
        }
    }
}
```
</details>

### Expected result

All dependencies defined in `Pipfile.lock` should be installed in the virtualenv. Expected set of dependencies:

```
$> pip freeze

attrs==19.3.0
boto3==1.12.39
botocore==1.15.49
certifi==2020.4.5.1
chardet==3.0.4
coverage==5.1
docutils==0.15.2
idna==2.9
importlib-metadata==1.6.0
jmespath==0.10.0
more-itertools==8.3.0
packaging==20.4
pluggy==0.13.1
py==1.8.1
pyparsing==2.4.7
pytest==5.4.1
pytest-cov==2.8.1
python-dateutil==2.8.1
requests==2.23.0
s3transfer==0.3.3
six==1.15.0
urllib3==1.25.9
wcwidth==0.1.9
zipp==3.1.0
zipstream-new==1.1.7
```
### Actual result

Only dependencies not being installed system-wide are installed in the virtualenv. Actual set of installed depedencies:

```
$> pip freeze

attrs==19.3.0
boto3==1.12.39
botocore==1.15.49
chardet==3.0.4
coverage==5.1
docutils==0.15.2
idna==2.9
jmespath==0.10.0
more-itertools==8.3.0
packaging==20.4
pluggy==0.13.1
py==1.8.1
pyparsing==2.4.7
pytest==5.4.1
pytest-cov==2.8.1
python-dateutil==2.8.1
requests==2.23.0
s3transfer==0.3.3
urllib3==1.25.9
wcwidth==0.1.9
zipstream-new==1.1.7
```

### Steps to replicate

1. Add some system-wide dependencies

```
root@209c93f34a0a:~# pip freeze

appdirs==1.4.4
certifi==2020.4.5.1
distlib==0.3.0
filelock==3.0.12
importlib-metadata==1.6.0
pipenv==2020.5.28
six==1.15.0
virtualenv==20.0.21
virtualenv-clone==0.5.4
zipp==3.1.0
```

2. Go to `Pipfile` enclosing directory

```
root@209c93f34a0a:~# cd /project/
```

3. Create new virtualenv

```
root@209c93f34a0a:/project# virtualenv -p python venv

created virtual environment CPython3.7.7.final.0-64 in 2288ms
  creator CPython3Posix(dest=/project/venv, clear=False, global=False)
  seeder FromAppData(download=False, pip=latest, setuptools=latest, wheel=latest, via=copy, app_data_dir=/home/node/.local/share/virtualenv/seed-app-data/v1.0.1)
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
```

4.  Activate virtualenv

```
root@209c93f34a0a:/project# source venv/bin/activate
```

5. Check if activated virtualenv is empty

```
(venv) root@209c93f34a0a:/project# pip freeze
```

6. Run `pipenv install` within the activated virtualenv

```
(venv) root@209c93f34a0a:/project# pipenv install --dev --deploy --ignore-pipfile

Courtesy Notice: Pipenv found itself running within a virtual environment, so it will automatically use that environment, instead of creating its own for any project. You can set PIPENV_IGNORE_VIRTUALENVS=1 to force pipenv to ignore that environment and create its own instead. You can set PIPENV_VERBOSITY=-1 to suppress this warning.
Installing dependencies from Pipfile.lock (59121c)…
  🐍   ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 21/21 — 00:00:23
```

7. Check what has been installed

```
(venv) root@209c93f34a0a:/project# pip freeze

attrs==19.3.0
boto3==1.12.39
botocore==1.15.49
chardet==3.0.4
coverage==5.1
docutils==0.15.2
idna==2.9
jmespath==0.10.0
more-itertools==8.3.0
packaging==20.4
pluggy==0.13.1
py==1.8.1
pyparsing==2.4.7
pytest==5.4.1
pytest-cov==2.8.1
python-dateutil==2.8.1
requests==2.23.0
s3transfer==0.3.3
urllib3==1.25.9
wcwidth==0.1.9
zipstream-new==1.1.7
```

-------------------------------------------------------------------------------

<details><summary>$ pipenv --support</summary>

Pipenv version: `'2020.5.28'`

Pipenv location: `'/usr/local/lib/python3.7/site-packages/pipenv'`

Python location: `'/usr/local/bin/python'`

Python installations found:

  - `3.7.7`: `/usr/local/bin/python3.7m`
  - `3.7.7`: `/usr/local/bin/python3`
  - `3.7.7`: `/usr/local/bin/python3.7`
  - `3.7.3`: `/usr/bin/python3.7m`
  - `3.7.3`: `/usr/bin/python3`
  - `3.7.3`: `/usr/bin/python3.7`
  - `2.7.16`: `/usr/bin/python2`
  - `2.7.16`: `/usr/bin/python2.7`

PEP 508 Information:

```
{'implementation_name': 'cpython',
 'implementation_version': '3.7.7',
 'os_name': 'posix',
 'platform_machine': 'x86_64',
 'platform_python_implementation': 'CPython',
 'platform_release': '4.19.76-linuxkit',
 'platform_system': 'Linux',
 'platform_version': '#1 SMP Fri Apr 3 15:53:26 UTC 2020',
 'python_full_version': '3.7.7',
 'python_version': '3.7',
 'sys_platform': 'linux'}
```

System environment variables:

  - `HOSTNAME`
  - `PYTHON_VERSION`
  - `PWD`
  - `HOME`
  - `LANG`
  - `GPG_KEY`
  - `TERM`
  - `PROJECT_PATH`
  - `SHLVL`
  - `PYTHON_PIP_VERSION`
  - `PYTHON_GET_PIP_SHA256`
  - `PYTHON_GET_PIP_URL`
  - `PATH`
  - `_`
  - `PIP_DISABLE_PIP_VERSION_CHECK`
  - `PYTHONDONTWRITEBYTECODE`
  - `PIP_SHIMS_BASE_MODULE`
  - `PIP_PYTHON_PATH`
  - `PYTHONFINDER_IGNORE_UNSUPPORTED`

Pipenv–specific environment variables:


Debug–specific environment variables:

  - `PATH`: `/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin`
  - `LANG`: `C.UTF-8`
  - `PWD`: `/home/node`


---------------------------

</details>


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Regression in 2020.05.28 -- pipenv omits installation of dependencies in enclosing virtualenv if they are installed system-wide #4276

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Uh oh!

Regression in 2020.05.28 -- pipenv omits installation of dependencies in enclosing virtualenv if they are installed system-wide #4276

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