Why "npm install" removes all package in node_modules?

The npm install command removes all packages in node_modules but not in package.json.

The npm's config (npm confg ls -l) is

long = true
metrics-registry = "https://registry.npmjs.org/"
scope = ""
user-agent = "npm/5.0.3 node/v7.4.0 win32 x64"

; globalconfig C:\Users\Nicola\AppData\Roaming\npm\etc\npmrc
production = true

; builtin config undefined
prefix = "C:\\Users\\Nicola\\AppData\\Roaming\\npm"

; default values
access = null
allow-same-version = false
also = null
always-auth = false
auth-type = "legacy"
bin-links = true
browser = null
ca = null
cache = "C:\\Users\\Nicola\\AppData\\Roaming\\npm-cache"
cache-lock-retries = 10
cache-lock-stale = 60000
cache-lock-wait = 10000
cache-max = null
cache-min = 10
cafile = undefined
cert = null
color = true
depth = null
description = true
dev = false
dry-run = false
editor = "notepad.exe"
engine-strict = false
fetch-retries = 2
fetch-retry-factor = 10
fetch-retry-maxtimeout = 60000
fetch-retry-mintimeout = 10000
force = false
git = "git"
git-tag-version = true
global = false
global-style = false
globalconfig = "C:\\Users\\Nicola\\AppData\\Roaming\\npm\\etc\\npmrc"
globalignorefile = "C:\\Users\\Nicola\\AppData\\Roaming\\npm\\etc\\npmignore"
group = 0
ham-it-up = false
heading = "npm"
https-proxy = null
if-present = false
ignore-prepublish = false
ignore-scripts = false
init-author-email = ""
init-author-name = ""
init-author-url = ""
init-license = "ISC"
init-module = "C:\\Users\\Nicola\\.npm-init.js"
init-version = "1.0.0"
json = false
key = null
legacy-bundling = false
link = false
local-address = undefined
loglevel = "notice"
logs-max = 10
; long = false (overridden)
maxsockets = 50
message = "%s"
; metrics-registry = null (overridden)
node-version = "7.4.0"
offline = false
onload-script = null
only = null
optional = true
package-lock = true
parseable = false
prefer-offline = false
prefer-online = false
; prefix = "C:\\Program Files\\nodejs" (overridden)
production = true
progress = true
proprietary-attribs = true
proxy = null
rebuild-bundle = true
registry = "https://registry.npmjs.org/"
rollback = true
save = true
save-bundle = false
save-dev = false
save-exact = false
save-optional = false
save-prefix = "^"
save-prod = false
scope = ""
scripts-prepend-node-path = "warn-only"
searchexclude = null
searchlimit = 20
searchopts = ""
searchstaleness = 900
send-metrics = false
shell = "C:\\WINDOWS\\system32\\cmd.exe"
shrinkwrap = true
sign-git-tag = false
sso-poll-frequency = 500
sso-type = "oauth"
strict-ssl = true
tag = "latest"
tag-version-prefix = "v"
timing = false

umask = 0
unicode = false
unsafe-perm = true
usage = false
user = 0

version = false
versions = false
viewer = "browser"

Other strange thing: the npm update and 'npm install --only=dev' works good but after executing this commad in PhpStorm (File -> Settings -> Laguanges and Framework -> Node.js ana NPM) I see listed only the devDependecies....Why?

via Webman