fix(status): report a project without a GitHub origin as absent

[ScriptedAlchemy]

mcp_suite status_behavior_test has failed on master since #2221 added github_source to tracedecay_status.

Root cause. The pinned markdown was missing the new github_source line. The payload was also untruthful: status reported a project with no GitHub origin as {"state":"not_observed",...}, while the #2250 doctor authority reads the same observation as GitHubSourceReadV1::Absent. not_observed has never shipped (it is not in v1.0.0-beta.54), so it is renamed in place.

Change

• tracedecay_status reports a project with no GitHub origin as {"state":"absent","reason":"the checkout has no GitHub origin, or its advisory owner has not mounted in this daemon"}.
• The CLI status filter now matches absent, so the human status still prints no GitHub line for such a project.
• The user guide's github_source table gains an absent row.
• The test asserts the exact github_source object and adds the **github_source:** {2 field(s)} markdown line.

Fail before / pass after. The test below failed with the updated test on master code and passes with the fix:

status_behavior_test.rs:180: assertion `left == right` failed
  left: Object {"reason": String("the checkout has no GitHub origin, or its advisory owner has not mounted in this daemon"), "state": String("not_observed")}
 right: Object {"reason": String("..."), "state": String("absent")}

Runtime journey. Debug tracedecay built from this change, one isolated daemon capped at 6 GB, and a fresh local git repo with no remote:

$ tracedecay init && cd src && tracedecay status --json --project-path ..
github_source: {"reason": "the checkout has no GitHub origin, or its advisory owner has not mounted in this daemon", "state": "absent"}
$ tracedecay status | grep -iE "github|error"   # no output (exit 1)

Local proof

• mcp_suite (full run): 574 passed, 0 failed. After rebasing onto 99b357d, status_behavior_test and mcp_cli_serve_test pass 18/18.
• cargo clippy -p tracedecay-runtime-core -p tracedecay-mcp -p tracedecay-cli -p tracedecay --all-targets -D warnings is clean with and without tracedecay/test-transport,test-helpers.
• cargo fmt --all -- --check is clean.

Fixes #2244

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[chatgpt-codex-connector]

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-26T20:15:22.603006Z	216c679	PR opened

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[chatgpt-codex-connector]

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Reviewed commit: 216c679566

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[chatgpt-codex-connector]

Preserve the unmounted state instead of claiming absence

When a checkout has a GitHub origin but its full advisory owner has not mounted—such as when indexing is disabled or there are no indexable files—github_source_status_v1 still returns None. This branch now reports state: "absent" even though the source exists, conflating an unavailable authority with a definitive absence; the reason on the next line explicitly acknowledges this second scenario. Keep an unmounted/not-observed state distinct from a checkout that actually lacks an origin.

AGENTS.md reference: AGENTS.md:L228-L229

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[chatgpt-codex-connector]

Continue accepting the previous not_observed response

When the updated CLI connects to a still-running daemon built from the parent revision, that daemon returns the placeholder { "state": "not_observed", ... }. Because this filter now excludes only absent, the placeholder is passed to serde_json::from_value::<GitHubSourceStatusV1>, which fails on the missing repository field and makes plain tracedecay status exit with an error during version skew. Filter both placeholder states, or decode them through a compatible typed response.

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