Replace string+normalize daemon timeout flags with a custom pflag.Value duration type

[peteski22]

The daemon timeout and interval flags are registered as strings, normalized and validated late in validateFlags, then re-parsed in buildAPIOptions/buildDaemonOptions. Normalization and validation are split across a per-flag table in validateFlags and each option builder, and durations are stored as string with an invariant (valid, positive duration) the type does not enforce. This shape is what allowed --timeout-mcp-shutdown to be validated but never applied until #284.

A custom pflag.Value duration type would normalize and validate once, at flag-parse time, and let the config carry time.Duration:

type durationSeconds struct{ d time.Duration }

func (v *durationSeconds) Set(s string) error {
	s = strings.TrimSpace(s)
	if _, err := time.ParseDuration(s); err != nil {
		if _, err2 := time.ParseDuration(s + "s"); err2 == nil {
			s += "s" // bare number -> seconds
		}
	}
	d, err := time.ParseDuration(s)
	if err != nil {
		return fmt.Errorf("must be a duration such as 30s or 1m")
	}
	if d <= 0 {
		return fmt.Errorf("must be positive")
	}
	v.d = d
	return nil
}

func (v *durationSeconds) String() string { return v.d.String() }
func (v *durationSeconds) Type() string   { return "duration" }

Registered with Flags().Var(...), this would:

• Normalize and validate once, when cobra parses the flag, before RunE — invalid input fails immediately with a per-flag error.
• Store time.Duration in the config struct, so buildAPIOptions/buildDaemonOptions read the value directly with no re-parse and no duplicated error handling.
• Remove the per-flag validation table, so a new duration flag inherits the behavior by type — eliminating the drift fix(cmd): accept bare seconds, reject negatives, and wire --timeout-mcp-shutdown for daemon timeouts #284 worked around.
• Stop validateFlags mutating config as a side effect.

Scope

• Every timeout/interval flag registration (StringVar -> Var).
• timeoutFlagConfig/intervalFlagConfig field types (string -> time.Duration).
• Both option builders (drop the re-parse).
• The config-file loaders and formatConfigInfo default rendering.
• Tests that currently assert string values such as "15s".
• Unifying with the config layer's config.Duration (JSON/TOML/YAML) type is the substantive design work — there should be one canonical duration representation across flags and config.

Open questions to settle

• Whether 0 should ever be valid for any duration flag. fix(cmd): accept bare seconds, reject negatives, and wire --timeout-mcp-shutdown for daemon timeouts #284 rejects non-positive at the CLI; the config Validate() methods already reject non-positive.
• Whether interval flags should also accept bare seconds. fix(cmd): accept bare seconds, reject negatives, and wire --timeout-mcp-shutdown for daemon timeouts #284 keeps --interval-mcp-health unit-required.
• Whether validateFlags should accumulate errors with errors.Join rather than returning the first.
• --help default rendering: with Var, the default shown comes from String(), so defaults must be seeded before registration.

pflag's built-in DurationVar cannot be reused because it rejects bare numbers. Follow-up from #284, which fixed the immediate bugs (bare-seconds normalization, positive validation, wiring --timeout-mcp-shutdown) and left this structural change as separate work.