Q:

Project organization and naming conventions

This is somewhat a follow-up to Repeating module name for each module component question. 
We've decided to follow the suggested in Best Practice Recommendations for Angular App Structure blog post angular project organization and naming conventions while building a small internal application for measuring connection quality.  
And this is what we've got at the moment:
$ tree -L 1
. 
├── app-config-service.js
├── app-config-service_test.js
├── app-connection-service.js
├── app-connection-service_test.js
├── app-controller.js
├── app-controller_test.js
├── app-countdown-directive.js
├── app-countdown-directive_test.js
├── app-footer-directive.js
├── app-footer-directive_test.js
├── app-footer-service.js
├── app-footer-service_test.js
├── app-math-service.js
├── app-math-service_test.js
├── app-stats-directive.js
├── app-stats-directive_test.js
├── app-status-directive.js
├── app-status-directive_test.js
├── app-status-service.js
├── app-status-service_test.js
├── app-time-directive.js
├── app-time-directive_test.js
├── app.css
├── app.js
├── bower_components
├── config.json
├── countdown.html
├── footer.html
├── img
├── index.html
├── ping
├── stats.html
└── status.html

As you can see, there are several directives, services, partials, single controller, module declaration file and couple config and app-specific unrelated to the topic files.  This really becomes a mess of files and is not quite readable and easy to work with. 
This is probably because we have only one single module and keep everything inside it. 
Is it okay to use the good old component-oriented approach and have special directories for services, controllers, directives and partials for such a simple app?  Does this mean that the new "Organized by feature" approach work only for non-trivial huge applications? 

A:

You say that you decided to "follow the suggested in Best Practice Recommendations for Angular App Structure blog post", but you don't seem to have followed it...

According to the recommended approach, each component/feature should be in its own directory (under a components directory). 
For the reasons pointed out by Gil Birman and also detailed in the aforementioned blog post as well as in Repeating module name for each module component, it makes more sense to organize the directories by feature (e.g. the foo-feature directory contains all directives, services, controllers, partials etc related to that feature) than organizing by type (e.g. all controllers in one directory, all services in another) etc. 

In any case, all the above are guidelines (more a way of thinking) and not a precise recipe or a deterministic algorithm that can decide for you where to place each file (e.g. is there going to be a components/lib/ directory, will a service go inside a feature's directory or under a components/common/ directory etc). 
You need to understand the guidelines (and what purpose/need the are trying to fulfil) and develop a convention that suits your team's style. 
There are times when you won't be sure where to place a file.  You can have a debate with the team, make a decision and go with that. 
This is totally normal (especially at first), but you'll find out that as time goes by, such cases will arise more and more rarely. 

That said, I would expect your directory and file structure to be more like that (making some assumptions about which services might be more generic/utility-like):
app/
|___ app.css
|___ app.js
|___ app-controller.js
|___ app-controller_test.js
|___ bower_components
|___ config.json
|___ index.html
|
|___ components/
|    |___ common/ or util/
|    |    |___ config-service.js
|    |    |___ config-service_test.js
|    |    |___ connection-service.js
|    |    |___ connection-service_test.js
|    |    |___ math-service.js
|    |    |___ math-service_test.js
|    |
|    |___ countdown/
|    |    |___ countdown.html
|    |    |___ countdown-directive.js
|    |    |___ countdown-directive_test.js
|    | 
|    |___ footer/
|    |    |___ footer.html
|    |    |___ footer-directive.js
|    |    |___ footer-directive_test.js
|    |    |___ footer-service.js
|    |    |___ footer-service_test.js
|    |
|    |___ img/
|    |    |___ ...
|    |
|    |___ stats/
|    |    |___ stats.html
|    |    |___ stats-directive.js
|    |    |___ stats-directive_test.js
|    | 
|    |___ status/
|    |    |___ status.html
|    |    |___ status-directive.js
|    |    |___ status-directive_test.js
|    |    |___ status-service.js
|    |    |___ status-service_test.js
|    |
|    |___ time/
|         |___ time-directive.js
|         |___ time-directive_test.js
|
|___ misc/
     |___ ping

