JERUSALEM — Israeli experts are nearing completion of an ambitious restoration of the five-century-old walls of Jerusalem, the holy city’s dominant architectural feature and a unique record of its eventful and troubled history.

The $5 million undertaking, which began in 2007, is set to be complete by the end of this year. The first restoration of the walls in nearly a century, it has required decisions about which of the walls’ many idiosyncrasies — the falcon nests, for example, the hundreds of machine-gun bullets, the botched restorations of years past — are flaws to be corrected, and which have earned a place in Jerusalem’s story and are thus worth preserving.