Do I need to manually create a migration for a HABTM join table?

You should do this in a migration of one of the tables, or in a separate migration if those migrations have been ran:

create_table :articles_tags, :id => false do |t|
  t.references :article, :tag
end

add_index :articles_tags, [:article_id, :tag_id]

This will create the table for you and the :id => false tells Rails not to add an id field to this table. There’s an index also, which will speed up lookups for this join table.

You could also generate a model (ArticlesTag) for this and do:

# article.rb
has_many :articles_tags
has_many :tags, :through => :articles_tags

# tag.rb
has_many :articles_tags
has_many :articles, :through => :articles_tags

# article_tag.rb
belongs_to :tag
belongs_to :article

And then create the table in the migration generated from the script/generate model articles_tag call.