Migrate versions declaration to manifest files

[cbeauchesne]

• cpp #1559
• .NET #1570
• golang #1563
• nodejs #1549
• java #1587
• php_appsec #1582
• php #1585
• python #1576
• ruby #1572
• agent #1591
• Do a final pass for leftovers #1591
• update the doc #1592
• Remove the temporary code for migration #1594