sam build deletes (package.json local path) source files

### Description
When using npm [local paths](https://docs.npmjs.com/files/package.json#local-paths) (ie a `package.json` dependency that is not in npm but rather on the local file system), `sam build` builds correctly the first time, on subsequent builds however, it deletes the *source files* in addition to the build files.

**tl;dr; Mitigation is to `rm -rf .aws-sam` every time prior to running `sam build`**

### Steps to reproduce
```
sam init #hello-world
cd sam-app

# Shared libs are common with APIG / Lambda since many tutorials indicate that each API should be its own lambda function
mkdir -p shared-libs
echo "{}" > shared-libs/package.json # Fake package for now
# Add a dependency on the shared-libs
cat > hello-world/package.json << PACKAGE_JSON
{
"name": "hello_world",
"version": "1.0.0",
"dependencies": {
"shared-libs": "file:../../../shared-libs"
}
}
PACKAGE_JSON

sam build # this one will succeed
sam build # this one will fail because the shared-libs directory has been deleted
```

### Observed result

```
$ sam build --debug
Telemetry endpoint configured to be https://aws-serverless-tools-telemetry.us-west-2.amazonaws.com/metrics
'build' command is called
No Parameters detected in the template
2 resources found in the template
Found Serverless function with name='HelloWorldFunction' and CodeUri='hello-world/'
Building resource 'HelloWorldFunction'
Loading workflow module 'aws_lambda_builders.workflows'
Registering workflow 'PythonPipBuilder' with capability 'Capability(language='python', dependency_manager='pip', application_framework=None)'
Registering workflow 'NodejsNpmBuilder' with capability 'Capability(language='nodejs', dependency_manager='npm', application_framework=None)'
Registering workflow 'RubyBundlerBuilder' with capability 'Capability(language='ruby', dependency_manager='bundler', application_framework=None)'
Registering workflow 'GoDepBuilder' with capability 'Capability(language='go', dependency_manager='dep', application_framework=None)'
Registering workflow 'GoModulesBuilder' with capability 'Capability(language='go', dependency_manager='modules', application_framework=None)'
Registering workflow 'JavaGradleWorkflow' with capability 'Capability(language='java', dependency_manager='gradle', application_framework=None)'
Registering workflow 'JavaMavenWorkflow' with capability 'Capability(language='java', dependency_manager='maven', application_framework=None)'
Registering workflow 'DotnetCliPackageBuilder' with capability 'Capability(language='dotnet', dependency_manager='cli-package', application_framework=None)'
Found workflow 'NodejsNpmBuilder' to support capabilities 'Capability(language='nodejs', dependency_manager='npm', application_framework=None)'
Running workflow 'NodejsNpmBuilder'
Running NodejsNpmBuilder:NpmPack
NODEJS packaging file:C:\Users\cheruvian\workspaces\sam-app\hello-world to C:\Users\CHERUV~1\AppData\Local\Temp\tmp3rug8kkf
executing NPM: ['npm.cmd', 'pack', '-q', 'file:C:\\Users\\cheruvian\\workspaces\\sam-app\\hello-world']
NODEJS packed to hello_world-1.0.0.tgz
NODEJS extracting to C:\Users\CHERUV~1\AppData\Local\Temp\tmp3rug8kkf\unpacked
NodejsNpmBuilder:NpmPack succeeded
Running NodejsNpmBuilder:CopyNpmrc
NodejsNpmBuilder:CopyNpmrc succeeded
Running NodejsNpmBuilder:CopySource
NodejsNpmBuilder:CopySource succeeded
Running NodejsNpmBuilder:NpmInstall
NODEJS installing in: C:\Users\cheruvian\workspaces\sam-app\.aws-sam\build\HelloWorldFunction
executing NPM: ['npm.cmd', 'install', '-q', '--no-audit', '--no-save', '--production']
NodejsNpmBuilder:NpmInstall failed
Traceback (most recent call last):
File "C:\Program Files\Amazon\AWSSAMCLI\runtime\lib\site-packages\aws_lambda_builders\workflows\nodejs_npm\actions.py", line 108, in execute
["install", "-q", "--no-audit", "--no-save", "--production"], cwd=self.artifacts_dir
File "C:\Program Files\Amazon\AWSSAMCLI\runtime\lib\site-packages\aws_lambda_builders\workflows\nodejs_npm\npm.py", line 85, in run
raise NpmExecutionError(message=err.decode("utf8").strip())
aws_lambda_builders.workflows.nodejs_npm.npm.NpmExecutionError: NPM Failed: npm ERR! code ENOLOCAL
npm ERR! Could not install from "..\..\..\shared-libs" as it does not contain a package.json file.

npm ERR! A complete log of this run can be found in:
npm ERR! C:\Users\cheruvian\AppData\Roaming\npm-cache\_logs\2020-04-30T08_36_46_582Z-debug.log

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Program Files\Amazon\AWSSAMCLI\runtime\lib\site-packages\aws_lambda_builders\workflow.py", line 269, in run
action.execute()
File "C:\Program Files\Amazon\AWSSAMCLI\runtime\lib\site-packages\aws_lambda_builders\workflows\nodejs_npm\actions.py", line 112, in execute
raise ActionFailedError(str(ex))
aws_lambda_builders.actions.ActionFailedError: NPM Failed: npm ERR! code ENOLOCAL
npm ERR! Could not install from "..\..\..\shared-libs" as it does not contain a package.json file.

npm ERR! A complete log of this run can be found in:
npm ERR! C:\Users\cheruvian\AppData\Roaming\npm-cache\_logs\2020-04-30T08_36_46_582Z-debug.log

Build Failed
Sending Telemetry: {'metrics': [{'commandRun': {'awsProfileProvided': False, 'debugFlagProvided': True, 'region': '', 'commandName': 'sam build', 'duration': 5577, 'exitReason': 'BuildError', 'exitCode': 1, 'requestId': 'fff5b25a-cb15-4e5b-9efe-edcdd1351b97', 'installationId': 'df7219e8-3473-48e3-9d07-ed6a44dee7f3', 'sessionId': '76da64b5-0cc0-464c-b398-519796eb1624', 'executionEnvironment': 'CLI', 'pyversion': '3.7.6', 'samcliVersion': '0.46.2'}}]}
Telemetry response: 200
Error: NodejsNpmBuilder:NpmInstall - NPM Failed: npm ERR! code ENOLOCAL
npm ERR! Could not install from "..\..\..\shared-libs" as it does not contain a package.json file.

npm ERR! A complete log of this run can be found in:
npm ERR! C:\Users\cheruvian\AppData\Roaming\npm-cache\_logs\2020-04-30T08_36_46_582Z-debug.log
```

### Expected result
1. Should *never* delete source files
1. Should build successfully every time

### Additional environment details (Ex: Windows, Mac, Amazon Linux etc)

1. OS: Windows 10 Pro
1. Shell: gitbash
2. `sam --version`: `SAM CLI, version 0.46.2`