v0.4.5

Bug pack rolling up findings from the v0.4.4 live test (paper eea5379b)
that completed end-to-end on a fresh pip install e2er. The pipeline
itself works; these are correctness + clarity fixes around it.

Lane C — Data

• Fix nested workspace path on --save-to (Lane C, replication
  correctness). The data_analyst subprocess runs with cwd at the paper's
  workspace dir; _resolve_workspace then resolved the relative default
  workspace_root="workspaces" against THAT cwd, so the CSV landed at
  workspaces/<id>/workspaces/<id>/data/. The model worked around this
  by emitting a _candidate_csv_paths fallback in estimation.py — a
  prompt-engineered band-aid for a pipeline bug. Fix: _resolve_workspace
  now prefers $E2ER_WORKSPACE_ROOT (claude_code injects the absolute
  path) over the relative settings default.
• Inject absolute workspace_root into the claude_code subprocess env
  (E2ER_WORKSPACE_ROOT) and use an absolute path as the subprocess cwd.
  Without both, the relative workspaces string can re-resolve at any
  nested call site.

Lane A — Pipeline

• Accept pipeline_mode as an alias for mode in CreatePaperRequest.
  e2er run --mode single_pass reached the API as pipeline_mode,
  which Pydantic silently dropped → server fell back to the default
  "iterative" → first-run log line falsely reported the wrong mode.
  Also fix src/cli_run.py to send the canonical mode field.
• Reword the first-run cap log line. "override=True" read like the
  server overrode the user's cap; it actually meant the user acknowledged
  the unproven (model, methodology, mode) tuple so the $1 floor was
  lifted to their requested cap. New format spells it out:
  cap=$20.00 (user_ack_unproven=True, first_run_floor=$1.00).

Cross-lane

• Label CLI-backend costs as estimates. Anyone running on
  claude_code / codex_cli / gemini_cli sees Sonnet-rate synthetic
  dollars even though the Max plan absorbs the actual cost. Startup log
  now warns once when a flat-rate backend is selected; the /api/papers/<id>
  usage payload carries a cost_is_estimate flag so dashboards can
  render the number with the right hedge.
• e2er migrate works on pip-installed wheels. Old code pointed at
  scripts/migrate.py which is excluded from the wheel. Moved to
  src/db/migrate.py (importable, ships in the wheel), reads SQL files
  via importlib.resources("sql") with a dev-checkout fallback.
• Drop the stale _SCRIPTS_DIR PATH entry on pip installs. Guarded
  with .exists() so the resolved PATH doesn't carry a non-existent
  site-packages/scripts/ directory that confused which-style probes
  inside the claude_code sandbox.