To merge bootloader and app SREC files so that in production you can program the device with a single .S file, you have to merge them in a slightly modified new SREC file.
Start the bootloader+app file with an "header" (S0) record containing an identification string of your choice, so in case it is sent to the bootloader by mistake it can be rejected instead of damaging it (if the bootloader executes directly from flash memory).
Then open in sequence the original srec files and append their their "data" (S1,S2 or S3) records in the new file, counting how many you append.
After you have sent all the "data" records from both files, append the the optional "data record count" (S5 or S6) record with the count of how many "data" records have been appended.
Finally append as "termination/start" (S7,S8 or S9) record the same record previously found as bootloader's "termination/start address".
The procedure described above can be automated with a small program.
It works correctly if the application's start address is always the same (and is directly encoded in the bootloader) AND if app and bootloader are stored in indipendently writable blocks/sections.
If you want to be able to update both app and bootloader sending them to an already installed bootloader (or if app and bootloader are mapped in the same block/section), you must encode the bootloader so it copies its code into RAM at boot and then executes the rest of itself from ram (so it can "rewrite itself" without hanging the microcontroller).
