When you issue a DIR command in a CMD prompt, the default behavior is to NOT show System and Hidden files.
To show everything, use the /A switch without any modifiers.
You can set the dircmd environment variable, to make /A the default.
I prefer using setting dircmd to /a /ogne, to also group directories first and sort by name and extension.
When you type dir /?, you receive the following short help:
Displays a list of files and subdirectories in a directory. DIR \[drive:\]\[path\]\[filename\] \[/A\]attributes \[/B\] \[/C\] \[/D\] \[/L\] \[/N\] \[/O\]sortorder \[/P\] \[/Q\] \[/S\] \[/T\]timefield \[/W\] \[/X\] \[/4\] \[drive:\]\[path\]\[filename\] Specifies drive, directory, and/or files to list. /A Displays files with specified attributes. attributes D Directories R Read-only files H Hidden files A Files ready for archiving S System files - Prefix meaning not /B Uses bare format (no heading information or summary). /C Display the thousand separator in file sizes. This is the default. Use /-C to disable display of separator. /D Same as wide but files are list sorted by column. /L Uses lowercase. /N New long list format where filenames are on the far right. /O List by files in sorted order. sortorder N By name (alphabetic) S By size (smallest first) E By extension (alphabetic) D By date/time (oldest first) G Group directories first - Prefix to reverse order /P Pauses after each screenful of information. /Q Display the owner of the file. /S Displays files in specified directory and all subdirectories. /T Controls which time field displayed or used for sorting timefield C Creation A Last Access W Last Written /W Uses wide list format. /X This displays the short names generated for non-8dot3 file names. The format is that of /N with the short name inserted before the long name. If no short name is present, blanks are displayed in its place. /4 Displays four-digit years Switches may be preset in the DIRCMD environment variable. Override preset switches by prefixing any switch with - (hyphen)--for example, /-W.For additional information, use tip 2815.