legacy application is one for which an executable is available, but not the source code. Therefore it cannot use the BOINC API and runtime system. However, such applications can be run using BOINC. Here's an example:

Compile the program 'worker' from the boinc_samples tree, producing (say) 'worker_5.10_windows_intelx86.exe'. This is the legacy app. If reads from stdin and writes to stdout; it also opens and reads a file 'in', and opens and writes a file 'out'. It takes one command-line argument: the number of CPU seconds to use.
Compile the program 'wrapper' from the boinc_samples tree, producing (say) 'wrapper_5.10_windows_intelx86.exe'. This program executes your legacy application, and acts as a proxy for it (to report CPU time etc.).
Create an application named 'worker', and a corresponding directory 'project/apps/worker'. In this directory, create a directory 'wrapper_5.10_windows_intelx86.exe'. Put the files 'wrapper_5.10_windows_intelx86.exe', and 'worker_5.10_windows_intelx86.exe' there.
In the same directory, create a file 'job.xml=job_1.12.xml' (1.12 is a version number) containing ".html_text(" worker_5.10_windows_intelx86.exe stdin stdout 10 ")." This file is read by 'wrapper'; it tells it the name of the legacy program, what files to connect to its stdin/stdout, and a command-line argument.
Create a workunit template file ".html_text(" 0 1 0 in 1 stdin 1000000000000 1000000000000 ")." and a result template file ".html_text(" 5000000 5000000 out stdout ")." Note that the files opened directly by the legacy program must have the <copy_file> tag.
Run update_versions to create an app version.

Run a script like

cp download/input `bin/dir_hier_path input`
cp download/input2 `bin/dir_hier_path input2`

bin/create_work -appname worker -wu_name worker_nodelete \
-wu_template templates/worker_wu \
-result_template templates/worker_result \
input input2

to generate a workunit.

Notes:

This requires version 5.5 or higher of the BOINC core client.
Multiple tasks per job is not implemented yet. Future versions of wrapper may allow you to run multiple applications in sequence (as specified in the job.xml file).
TODO: provide a way for projects to supply an animated GIFF which is shown (with user/team credit text) as screensaver graphics.

To understand how all this works: at the beginning of execution, the file layout is: "; list_start(); list_heading_array(array("Project directory", "slot directory")); list_item_array(array( "job_1.12.xml
input
input2
worker_5.10_windows_intelx86.exe
wrapper_5.10_windows_intelx86.exe ", " in (copy of project/input)
job.xml (link to project/job_1.12.xml)
stdin (link to project/input2)
stdout (link to project/worker_nodelete_0)
worker_5.10_windows_intelx86.exe (link to project/worker_5.10_windows_intelx86.exe)
wrapper_5.10_windows_intelx86.exe (link to project/wrapper_5.10_windows_intelx86.exe) " )); list_end(); echo " The wrapper program executes the worker, connecting its stdin to project/input2 and its stdout to project/worker_nodelete_0. The worker program opens 'in' for reading and 'out' for writing.

When the worker program finishes, the wrapper sees this and exits. Then the the BOINC core client copies slot/out to project/worker_nodelete_1. "; page_tail(); ?>