chore: officially migrate to submodule (#4502)

* remove apps/core and apps/fern

* fix precommit

* add submodule updates in workflows

* submodule

* remove core tests

* update core revision

* Add submodules: true to all GitHub workflows

- Ensure all workflows can access git submodules
- Add submodules support to deployment, test, and CI workflows
- Fix YAML syntax issues in workflow files

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* remove core-lint

* upgrade core with latest main of oss

---------

Co-authored-by: Claude <noreply@anthropic.com>

alembic/versions/56254216524f_add_custom_headers_to_mcp_server.py

@@ -1,40 +0,0 @@
-"""add_custom_headers_to_mcp_server
-
-Revision ID: 56254216524f
-Revises: 60ed28ee7138
-Create Date: 2025-07-02 14:08:59.163861
-
-"""
-
-from typing import Sequence, Union
-
-import sqlalchemy as sa
-
-from alembic import op
-from letta.settings import settings
-
-# revision identifiers, used by Alembic.
-revision: str = "56254216524f"
-down_revision: Union[str, None] = "60ed28ee7138"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def upgrade() -> None:
-    # Skip this migration for SQLite
-    if not settings.letta_pg_uri_no_default:
-        return
-
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column("mcp_server", sa.Column("custom_headers", sa.JSON(), nullable=True))
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # Skip this migration for SQLite
-    if not settings.letta_pg_uri_no_default:
-        return
-
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_column("mcp_server", "custom_headers")
-    # ### end Alembic commands ###