Lockfile and other improvements

[elcritch]

Changes:

• Add shallow cloning and fetching by default which speeds up cloning quite a bit (submodules are also shallow)

• Add --full option which will do a full clone and call --unshallow when needed on existing shallow clones

• Add "version" to lockfiles so changed can display versions diffs

• Change lockfiles to use $deps/deps_path or $workspace/pkg for dirs so that atlas replay works in scenarios where users have depsDir defined, otherwise lockfiles do weird things

• Change lockfile nimCfg and nimble.contents to use array of lines for better git diff's and ease of manual modifications / reviews (the previous format is automatically converted)

• atlas replay --cfgHere should actually work and not trample the commits by using the packages in the lockfile to create the nim.cfg with users local depsDirs

• Some logging fixes

Updated lockfile format example

{
  "items": {
    "assume": {
      "dir": "$deps/assume",
      "url": "https://github.com/disruptek/assume",
      "commit": "ebed5f2b726134400a4aca489d39e54a2e6dcd95",
      "version": "0.7.2"
    },
    "pixie": {
      "dir": "$deps/pixie",
      "url": "https://github.com/treeform/pixie",
      "commit": "523b364fcaa288d23ecb3f34c795da97d3637117",
      "version": "5.0.6"
    },
  },
  "nimcfg": [],
  "nimbleFile": {
    "filename": "figuro.nimble",
    "content": [
      "version       = \"0.6.0\"",
      "author        = \"Jaremy Creechley\"",
      "description   = \"UI Engine for Nim\"",
      "license       = \"MIT\"",
      "srcDir        = \".\"",
      "",
      "# Dependencies",
      "",
      "requires \"nim >= 1.6.5\"",
      "requires \"pixie >= 5.0.1\"",
      ""
    ]
  },
  "hostOS": "macosx",
  "hostCPU": "arm64",
  "nimVersion": "2.0.0 a488067a4130f029000be4550a0fb1b39e0e9e7c",
  "gccVersion": "",
  "clangVersion": ""
}