What process happens when there is a system optimization? My question is the following: Not long ago I was moving apk, data and .dex files to the directories / data, and they did not show the applications I had manually installed, if not until I rebooted on the device and a message appeared saying "optimize the system" from the moment I was curious about this.

My purpose is to learn what happens in this process and to know how to be able to repeat it manually.

If you know anything about this, I'll be happy to hear your comments and answers.
What is Android doing when it says “optimizing apps/system”?

Basically the android system will be creating an optimised version of each application. This process makes each app start as fast as possible with the new Android version.


  While it says ‘optimising,’ operating system generates ‘odex’ files
  for your apps from scratch. As a simple explanation, odex files can
  help the system boot faster and reduces the time needed for launching
  applications.


Apk files and odex files


  The longer story is that when an APK file is added to your Android
  system, it’s not actually stored that way. It’s converted to something
  called an “odex” file.


The Android OS does not store apps as is after installation (i.e., one single APK file). An optimized version of the app is stored in the Dalvik cache — called the odex file.”

What Is an Odex File?

In Android file system, applications come in packages with the extension .apk. These application packages, or APKs contain certain .odex  (Optimized Dalvik EXecutable) files whose supposed function is to save space. These odex files are actually collections of parts of an application that are optimized before booting. Doing so speeds up the boot process, as it preloads part of an application. On the other hand, it also makes hacking those applications difficult because a part of the coding has already been extracted to another location before execution.

Deodex

Deodexing is basically repackaging of these APKs in a certain way, such that they are reassembled into classes.dex files (Dalvik EXecutable).


  By doing that, all pieces of an application package are put together
  back in one place, thus eliminating the worry of a modified APK
  conflicting with some separate odexed parts.


In summary, Deodexed ROMs (or APKs) have all their application packages put back together in one place, allowing for easy modification such as theming. Since no pieces of code are coming from any external location, custom ROMs or APKs are always deodexed to ensure integrity.

There are several explanations on how this works:


  In Android, applications come in packages with the extension  .apk.
  These application packages, or APKs contain certain .odex files whose
  supposed function is to save space. These ‘odex’ files are actually
  collections of parts of an application that are optimized before
  booting. Doing so speeds up the boot process, as it preloads part of
  an application.
  
  Android OS uses a Java-based virtual machine for running applications,
  called the Dalvik Virtual Machine. A deodexed, or .dex file contains
  the cache used by this virtual machine (referred to as Dalvik-cache)
  for a program, and it is stored inside the APK. An .odex file, on the
  other hand, is an optimized version of this same .dex file that is
  stored next to the APK as opposed to inside it. Android applies this
  technique by default to all the system applications. Now, when an
  Android-based system is booting, the davlik cache for the Davlik VM is
  built using these .odex files, allowing the OS to learn in advance
  what applications will be loaded, and thus speeds up the booting
  process. By deodexing these APKs, a developer actually puts the .odex
  files back inside their respective APK packages. Since all code is now
  contained within the APK itself, it becomes possible to modify any
  application package without conflicting with the operating system’s
  execution environment.


How to do the process manually;

If you want to manually optimise your apks, there are some options:


You could try using  using applications like Lucky patcher
Alternatively with Windows you can zip-align them with 
Apk decomplier (apk sign tool)


Acknowledgements


What Is Odex And Deodex In Android
What is Android doing when, after an upgrade, it tells you it's "optimizing" the apps?
http://alvinalexander.com/android/what-android-doing-optimizing-apps-after-system-upgrade-restart