In TaskPaper versions up until 2.1 you didn't need to indent tasks and notes under projects for those tasks and notes to belong to the project. Tasks and notes would belong to a project even if they were at the same indentation level as the project. But in version 2.2 (still in development as of Jan 8, 2009) the file format is changing so that it's required that you indent those tasks under the project for them to be considered part of the project. This script will convert a document from the old style format to the new style format that requires indentation:
tell application "TaskPaper"
tell front document
repeat with each in entries
if not (entry type of each = project type) then
set text line of each to tab & text line of each
end if
end repeat
end tell
end tell
See this forum topic for more discussion on the change.
