feat(config): every CLI setting is now settable in config.json

[Emasoft]

Wiring status

16 of the 20 settings are wired end-to-end on this branch. The remaining 4 — bash-timeout, subagent-idle-timeout, subagent-idle-kill-after, max-concurrent-llm-requests — have their config-layer fields, resolvers, and tests in place, but their CLI application points (tool.SetShellTimeout, the orchestrator SetIdlePolicy, client.SetLLMConcurrency) arrive with the sibling PRs that introduce those flags (#130, #131, #132). The wiring will be added as those merge — that is inherent to the independent-PR structure, not an omission.

Every flag that makes sense to persist now has a config.json equivalent: 20 new kebab-case entries mirroring the flag names exactly — --bash-timeout → "bash-timeout", --system-prompt → "system-prompt", and so on.

Precedence is explicit and enforced

explicitly-passed flag > config.json > built-in default. The explicitly-passed set is built with flag.Visit, so only flags actually typed on the command line override the config file — a flag left at its Go default doesn't shadow config. max-stream-retries keeps its env layer: flag > env > config > default.

Typing rules

• durations are strings ("45s", "2m") — no unit confusion
• default-true bools and meaningful-zero ints are tri-state pointers, so config can distinguish "unset" from "explicitly false/zero"

Each flag's -h usage string names its config.json key.

Honest scope

16 of the 20 are wired end-to-end on this branch. The other 4 — bash-timeout, subagent-idle-timeout, subagent-idle-kill-after, max-concurrent-llm-requests — have fields, resolvers, and tests at the config layer; their CLI application points ride with the sibling PRs that add those flags.

Dependency note: docs/config-reference.md ships with the strict-parsing PR.

Testing

$ go test -count=1 -race ./...
ok  	late/cmd/late	3.091s
?  	late/cmd/mcp-run	[no test files]
ok  	late/internal/agent	2.026s
?  	late/internal/assets	[no test files]
ok  	late/internal/client	1.558s
ok  	late/internal/common	3.278s
ok  	late/internal/config	3.077s
ok  	late/internal/executor	7.905s
ok  	late/internal/git	2.425s
ok  	late/internal/mcp	1.855s
ok  	late/internal/orchestrator	4.318s
?  	late/internal/pathutil	[no test files]
ok  	late/internal/plugin	11.884s
ok  	late/internal/session	3.304s
ok  	late/internal/skill	3.391s
ok  	late/internal/tool	3.337s
ok  	late/internal/tool/ast	3.702s
ok  	late/internal/tui	8.807s

exit 0 — all 18 packages green (15 ok, 3 without test files).