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Doubt 1:
Is there any way to store a data inside an executable on run time.
For example in C If I create a simple database which asks an employee to enter his details and can see his profile whenever he wants.
No. Executables are locked while they are running. There is no way to write to the file while the code is running.
Also, the problem of writing data to the .EXE is hideously complex.
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what I have did?
To my knowledge(at present) I would create a file for every employee and whenever he types his Id it can open the specific file and show the details using file handling.But how can I store the employee details within the executable.
This makes no sense at all. I have no idea what the "types his ID it can open the specific file..." means. Types an ID where? In the application that is in this .EXE you're customizing?
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Doubt 3:
How to make my program certified?
For example when I manifest my program it prompts the user for administrator permission.In that I found "publisher: unknown" How can I give my name ?
Certified by who and for what purpose? The application apparently requires admin privileges to run, but what did you do to make that happen? Did you create a manifest in the project? Did you do something in the code, like try to write something to the HKEY_LOCAL_MACHINE registry? What does this app do?
Signing your code so that the publisher field is filled in does not mean that it won't ask for admin permissions.