fix(mcp): index a just-added file on codedb_read miss

codedb_index told agents to prefer outline/read first, but codedb_read
disk-fell-back via getContent() and never called indexMissingFile.
Search and symbol then returned 0 hits for a file the agent had just
read. Index before getContent, keep ranged/raw on extractLines so #632
stays byte-exact, and cover the agent route in E2E scenario 6.

Co-Authored-By: Codegraff <blackfloofie@codegraff.com>