Calling cache:clear command now works by this scheme:

1. Creating temporary kernel in temporary file
2. Booting temporary kernel (due boot, kernel warming up the cache)
3. Move warmed up temporary dir to real cache dir with replacing usages of temporsry kernel class to user's kernel class

While building container, kernel adds to ContainerBuilder instance ObjectReource of itself ($this). Adding object resource acually means adding file with class, and files with parents of class as FileResource. Because building of container making by temporary kernel, file with it's class is temporary file, created on step 1. So, temporary file (which is actually deleted on step 1) added to metadata. This means, that next request with debug environment will rebuild just warmed up cache, because metadata contains reference to temporary file, which does not exists.