How to setup phpStorm for debug two projects at the same time?

Hi! It seems that due to the thread size we've lost an important detail here - xdebug.remote_connect_back is set to 1.
When the initial connection comes from the host to the VM, it uses the host address to sent debug data back.
But when the app connects to API, it's a localhost connection! So it sends data to localhost.
Please remove remote_connect_back completely and restart Apache. Would that help?

No :( if I set that option to 0 it does not connect back to the IDE. The xDebug setup looks like:

[xdebug] 
xdebug.idekey="PHPSTORM" 
xdebug.remote_enable = 1 
xdebug.remote_autostart = 0 
xdebug.remote_connect_back = 0 
xdebug.remote_port = 9001 
xdebug.remote_log="/var/log/xdebug.log" 
xdebug.remote_handler = "dbgp" 
;xdebug.remote_host=192.168.50.4 
 
xdebug.remote_addr_header = "HTTP_X_XDEBUG_REMOTE_ADDRESS" 

See logs below:

Log opened at 2018-05-29 18:54:22 
I: Connecting to configured address/port: localhost:9001. 
E: Could not connect to client. :-( 
Log closed at 2018-05-29 18:54:22 
 
Log opened at 2018-05-29 18:54:23 
I: Connecting to configured address/port: localhost:9001. 
E: Could not connect to client. :-( 
Log closed at 2018-05-29 18:54:23 
 
Log opened at 2018-05-29 18:54:23 
I: Connecting to configured address/port: localhost:9001. 
E: Could not connect to client. :-( 
Log closed at 2018-05-29 18:54:23 
 
Log opened at 2018-05-29 18:54:56 
I: Connecting to configured address/port: localhost:9001. 
E: Could not connect to client. :-( 
Log closed at 2018-05-29 18:54:56 
 
Log opened at 2018-05-29 18:54:56 
I: Connecting to configured address/port: localhost:9001. 
E: Could not connect to client. :-( 
Log closed at 2018-05-29 18:54:56 

Could you please confirm with phpinfo() that the parameter has been set to 0?
It can be a wrong .ini file (e.g. the CLI one) or you did not restart Apache so that the changes weren't applied.
Otherwise, it looks like pure magic.

Confirmed, is off

Here is some extra info regarding how the box is configured using Vagrant not sure if this could help:

# -*- mode: ruby -*-
# vi: set ft=ruby :

Vagrant.configure("2") do |config|
 config.vm.box = "CentOS-6.5-x86_64"
 config.vm.box_url = "centos65-x86_64-20131205.box"
 
 config.vm.provision :shell, :path => "bootstrap.sh" 
 
 config.vm.network "private_network", ip: "192.168.50.4"
 config.vm.network :forwarded_port, host: 8080, guest: 80
 config.vm.network "forwarded_port", host: 33060, guest: 3306
 
 config.vm.synced_folder "../../www", "/vagrant", :owner=>"apache", :group=>"apache"
 config.vm.synced_folder "../../media/", "/media" , :owner=>"root", :group=>"root"
 
 config.vm.provider :virtualbox do |vb|
 vb.customize ["modifyvm", :id, "--memory", 2048]
 vb.customize ["modifyvm", :id, "--natdnshostresolver1", "on"]
 vb.customize ["modifyvm", :id, "--natdnsproxy1", "on"]
 end
end

Oh, I didn't notice that the xdebug.remote_host parameter is commented out. Why?
And the value of the parameter is also questionable
For me, in my Vagrant setup, this parameter is set to the host IP address. If you're using NAT in Vagrant (it seems that you are), you should do the same.

Update: Just saw your message. So, what IP address can the VM use to connect to the host? You should use that one.

It was commented because I was trying different configurations for xDebug. I have followed your suggestions and now it seems to be working (see logs below) however it does not step into the breakpoints for API app not sure what else I am missing here:

Log opened at 2018-05-29 19:34:11
I: Connecting to configured address/port: 192.168.56.1:9001.
I: Connected to client. :-)
-> <init xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" fileuri="file:///vagrant/html/api/public/index.php" language="PHP" protocol_version="1.0" appid="11604" idekey="PHPSTORM"><engine version="2.2.7"><![CDATA[Xdebug]]></engine><author><![CDATA[Derick Rethans]]></author><url><![CDATA[http://xdebug.org]]></url><copyright><![CDATA[Copyright (c) 2002-2015 by Derick Rethans]]></copyright></init>

<- feature_set -i 1 -n show_hidden -v 1
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="feature_set" transaction_id="1" feature="show_hidden" success="1"></response>

<- feature_set -i 2 -n max_depth -v 1
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="feature_set" transaction_id="2" feature="max_depth" success="1"></response>

<- feature_set -i 3 -n max_children -v 100
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="feature_set" transaction_id="3" feature="max_children" success="1"></response>

<- feature_set -i 4 -n extended_properties -v 1
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="feature_set" transaction_id="4" status="starting" reason="ok"><error code="3"><message><![CDATA[invalid or missing options]]></message></error></response>

<- feature_set -i 5 -n notify_ok -v 1
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="feature_set" transaction_id="5" status="starting" reason="ok"><error code="3"><message><![CDATA[invalid or missing options]]></message></error></response>

<- stdout -i 6 -c 1
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="stdout" transaction_id="6" success="1"></response>

<- status -i 7
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="status" transaction_id="7" status="starting" reason="ok"></response>

<- step_into -i 8
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="step_into" transaction_id="8" status="break" reason="ok"><xdebug:message filename="file:///vagrant/html/api/public/index.php" lineno="21"></xdebug:message></response>

<- eval -i 9 -- aXNzZXQoJF9TRVJWRVJbJ1BIUF9JREVfQ09ORklHJ10p
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="eval" transaction_id="9"><property address="140735422311104" type="bool"><![CDATA[0]]></property></response>

<- eval -i 10 -- aXNzZXQoJF9TRVJWRVJbJ1NFUlZFUl9OQU1FJ10p
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="eval" transaction_id="10"><property address="140735422311104" type="bool"><![CDATA[1]]></property></response>

<- eval -i 11 -- KHN0cmluZykoJF9TRVJWRVJbJ1NFUlZFUl9OQU1FJ10p
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="eval" transaction_id="11"><property address="140735422311104" type="string" size="7" encoding="base64"><![CDATA[YXBpLmRldg==]]></property></response>

<- eval -i 12 -- KHN0cmluZykoJF9TRVJWRVJbJ1NFUlZFUl9QT1JUJ10p
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="eval" transaction_id="12"><property address="140735422311104" type="string" size="2" encoding="base64"><![CDATA[ODA=]]></property></response>

<- eval -i 13 -- KHN0cmluZykoJF9TRVJWRVJbJ1JFUVVFU1RfVVJJJ10p
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="eval" transaction_id="13"><property address="140735422311104" type="string" size="25" encoding="base64"><![CDATA[L3YxL2RvY3VtZW50cy9nZXRfYnlfaWQvMQ==]]></property></response>

<- run -i 14
-> <stream xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" type="stdout" encoding="base64"><![CDATA[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]]></stream>

-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="run" transaction_id="14" status="stopping" reason="ok"></response>

<- stop -i 15
-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="stop" transaction_id="15" status="stopped" reason="ok"></response>

Log closed at 2018-05-29 19:34:12

-> <stream xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" type="stdout" encoding="base64"><![CDATA[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]]></stream>

-> <response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="run" transaction_id="46" status="stopping" reason="ok"></response>

<- run -i 47
Log closed at 2018-05-29 19:34:12

@Eugene, I have found the latest issue which is for some reason the domain internally is changed to dev and the port to 80 so api.localhost:8080 from inside the box is api.dev. In other words:

• From outside the API can be accessed like: api.localhost:8080 (this is how I had setup the Server configuration)
• From inside the API can be accessed like: api.dev (since a cURL call happen inside the box, changing the server configuration makes it to work)

Thanks a lot for your patience and time!!

Wonderful! Thank you for the update, I am happy we've finally sorted this out.