Why npm tries to find package.json in the wrong directory? - angularjs

Question

I'm having a web app with TypeScript, Angular and several dependencies.
npm of course is here also.
package.json was introduced to the project from the begging by npm init and right now it looks like that:
{
"name": "myApp",
"version": "0.0.8-d",
"description": "Web App",
"author": "Author",
"license": "ISC",
"repository": {
"type": "git",
"url": "MYURL"
},
"bugs": {
"url": "MYURL"
},
"homepage": "MYURL",
"browserify": {
"transform": [
"debowerify"
]
},
"dependencies": {
"malihu-custom-scrollbar-plugin": "^3.1.3"
},
"devDependencies": {
"browserify": "~13.0.0",
"connect-history-api-fallback": "^1.2.0",
"connect-modrewrite": "^0.8.2",
"debowerify": "~1.2.0",
"gulp": "^3.9.1",
"gulp-autoprefixer": "^3.1.0",
"gulp-clean-css": "^2.0.4",
"gulp-concat": "^2.6.0",
"gulp-connect": "^3.2.2",
"gulp-less": "^3.0.5",
"gulp-ng-annotate": "^2.0.0",
"gulp-sass": "^2.2.0",
"gulp-sourcemaps": "^1.6.0",
"gulp-typescript": "^2.12.2",
"gulp-uglify": "^1.5.3",
"jasmine": "^2.4.1",
"run-sequence": "^1.1.5",
"typescript": "^1.8.9",
"vinyl-source-stream": "^1.1.0"
},
"scripts": {
"test": "echo \"Error: no test specified\" && exit 1"
}
}
Also my file structure is like this:
Root
|-- tscode
|-- compiled
|-- html_files
|-- node_modules
|-- libs
| package.json
This think is that npm seems to work fine, everything is installed correctly I can add/remove dependencies BUT always I'm getting this working:
npm WARN enoent ENOENT: no such file or directory, open '/Projects/MyApp/tscode/package.json'
package.json is on the root folder as it should but still I'm getting this warning which is very annoying. As you can see npm searching for the json file in a folder one level inside instead on the root.
Also if I do:
npm list --depth=0
Then I'm getting a correct list of my dependencies BUT also: -> /Projects/MyApp/innerfolder extraneous error: ENOENT: no such file or directory, open '/Projects/MyApp/tscode/package.json
Any ideas?
Node version: v5.10.1
npm version: 3.8.5
Note: This is happening to everyone in my team regardless OS.
UPDATE: It seems that there is a bug with npm. There are some open issues at npm repository such as:
https://github.com/npm/npm/issues/9633
https://github.com/npm/npm/issues/10004
If something change I'll update the question with an answer (if provided)

Answer 1

Try this :
Delete node_modules folder
Then run :
$ npm cache clean
$ npm install