Commiting multiple files to github over API

github.js

'use strict';

var Octokat = require('octokat');
var extend = require('lodash/object/assign');

var defaults = {
  branchName: 'master',
  token: '',
  username: '',
  reponame: ''
};

function init(options) {
  options = extend({}, defaults, options);
  var head;

  var octo = new Octokat({
    token: options.token
  });
  var repo = octo.repos(options.username, options.reponame);

  function fetchHead() {
    return repo.git.refs.heads(options.branchName).fetch();
  }

  function fetchTree() {
    return fetchHead().then(function(commit) {
      head = commit;
      return repo.git.trees(commit.object.sha).fetch();
    });
  }

  function commit(files, message) {
    return Promise.all(files.map(function(file) {
      return repo.git.blobs.create({
        content: file.content,
        encoding: 'utf-8'
      });
    })).then(function(blobs) {
      return fetchTree().then(function(tree) {
        return repo.git.trees.create({
          tree: files.map(function(file, index) {
            return {
              path: file.path,
              mode: '100644',
              type: 'blob',
              sha: blobs[index].sha
            };
          }),
          basetree: tree.sha
        });
      });
    }).then(function(tree) {
      return repo.git.commits.create({
        message: message,
        tree: tree.sha,
        parents: [
          head.object.sha
        ]
      });
    }).then(function(commit) {
      return repo.git.refs.heads(options.branchName).update({
        sha: commit.sha
      });
    });

  }

  return {
    commit: commit
  };
}

module.exports = init;

usage.js

'use strict';

var github = require('./github');

var api = github({
  username: 'YOUR_USERNAME',
  token: 'API_TOKEN', // created here https://github.com/settings/applications#personal-access-tokens
  reponame: 'BRANCH_NAME'
});

api.commit([{
  path: 'test/file1.md',
  content: '# File1'
}, {
  path: 'test/file2.md',
  content: '# File2'
}], 'test commit via api'); // returns a promise

Update: Works well as of April 2021 :-)

the same is possible to delete multiple files at once

delete: function(files, message) {
    return fetchTree()
      .then(function(tree) {
        return repo.git.trees.create({
          tree: files.map(function(file) {
            return {
              path: file.path,
              mode: '100644',
              type: 'blob',
              sha: null
            };
          }),
          base_tree: tree.sha
        });
      })
      .then((tree) => {
        return repo.git.commits.create({
          message: message,
          tree: tree.sha,
          parents: [ head.object.sha ]
        });
      })
      .then((commit) => {
        return repo.git.refs.heads(GITHUB_BRANCH).update({
          sha: commit.sha
        });
      })
  }

just for the sake of completeness...renameDir. It is not an easy task. You must delete all files in the directory which you want to rename and create a new tree with the SHA of the deleted tree

  renameDirectory: async function(fromDir, toDir, message) {
    let parentDir = path.dirname(fromDir)
    let parentSha = null
    let dirSha = null
    return fetchTree().then( (tree) => {
      parentSha = tree.sha
      return repo.contents(parentDir).fetch()
    }).then(function(infos) {
      let item = infos.items.find( item => item.path===fromDir )
      dirSha = item.sha
      return repo.git.trees(dirSha).fetch({recursive:true});
    }).then(function({tree}) {
      // create the "tree" with "sha:null" to delete all files below the old directory
      //
      const newTree = tree.filter(({ type }) => type === TYPE.BLOB)
                              .map(({ path, mode, type }) => ( { path: `${fromDir}/${path}`, sha: null, mode, type }));
      // create a tree with the sha of the delete directory....inherits the content.
      //
      newTree.push( {
        path: toDir,
        mode: '040000',
        type: 'tree',
        sha: dirSha
      })
      // create the new folder and delte the files in the old folder.
      //
      return repo.git.trees.create({
        tree: newTree,
        base_tree: parentSha
      });
    }).then(function(tree) {
      return repo.git.commits.create({
        message: message,
        tree: tree.sha,
        parents: [ head.object.sha ]
      });
    }).then(function(commit) {
      return repo.git.refs.heads(GITHUB_BRANCH).update({
        sha: commit.sha
      });
    });
  }