fix(cli): make spec and dataset file errors actionable

[Birfy]

Closes #205.

Reproduction

Using a freshly built wheel installed into a separate Python 3.12 virtual environment, outside the checkout, agentdescent plan missing.json and a spec with a trailing comma exited 1 with raw tracebacks. Dataset JSONL decoded each physical line separately and could only report decoder line 1.

Changes

• Translate file read/UTF-8/JSON decode failures into SpecError at the spec/dataset input boundary only.
• Include path, decoder message, line and column; JSONL counts physical lines, including blanks.
• Reject non-object JSON specs with a clear input error.
• Preserve existing CLI output contracts (spec read errors on stderr, plan validation errors in the response), valid inputs, and engine behavior.
• Add 27 regressions and recovery documentation.

Verification

• 90 focused tests pass: tests/test_spec_file_errors.py, tests/test_evolvespec.py, tests/test_runstore_cli.py.
• Independent review: no blockers; separately checked permissions, CRLF/CR JSONL line numbers, and unrelated RuntimeError propagation.
• Rebuilt installed wheel: malformed/missing spec exit 2 without traceback; broken JSONL reports physical line 4; offline demo exit 0.
• Full local suite: 3022 passed, 56 skipped, 19 known environment failures (18 nested sandbox/NETLINK_ROUTE and one Chromium PDF); no new failures or tests weakened.
• Exact head 2931d628492847942fb32887aa6a03a6b7fe2c15: all four Python 3.9/3.10/3.11/3.12 jobs passed full tests, wheel build and wheel smoke; strict docs CI passed. Local docs build did not complete (execution approval review cancelled); the same strict build succeeded in CI.

No provider calls, engine changes, release, or merge.

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-10T03:10:04.951975Z	2931d62	Draft marked ready

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