sync push: write adopted-by-id configs back into the manifest (follow-up to #482)

[padak]

Follow-up to #482 / PR #494, from the non-blocking review findings.

NB-1: adopted config is never written back into the manifest

When an untracked _config.yml is adopted via the id-matching guard (its _keboola.config_id resolves on the target branch and is unclaimed by the manifest) and pushed as modified, push_update() succeeds but the post-update manifest hash refresh finds no entry, so no manifest writeback happens. The state self-heals on the next sync pull (the config is in the remote listing, is_new → entry written), but until then:

• a local deletion of that file is not detected as deleted (it is not in tracked_keys),
• every sync diff/push re-derives the adopt decision instead of reading a stable manifest entry.

Suggested fix: after a successful adopted-by-id push_update, append a ManifestConfiguration entry (analogous to writeback_create_config_in_manifest) with fresh pull_hash/pull_config_hash.

NB-3: E2E test for the branch-switch-then-push regression

tests/test_e2e.py has test_sync_diff_branch_override but not the #482 sequence (pull main → pull dev branch → push with zero edits → assert no_changes). The fix was verified manually against a live project (pre-fix dry-run showed phantom added entries, post-fix push was a no-op); an automated E2E test needs a disposable dev branch created/deleted by the harness.

NB-2: gotcha entry at release time

When the next version is cut, add a (since vX.Y.Z) gotcha to plugins/kbagent/skills/kbagent/references/gotchas.md (and the keboola-expert inline gotchas if warranted): pre-fix versions duplicate branch-inherited configs on sync push after branch use + pull; agents on older installs should upgrade before pushing on a dev branch.

[padak]

Shipped in v0.72.0 (PR #506). Status per finding:

• NB-1 (adopted config never written back into the manifest): fixed. After a successful adopted-by-id push_update, when no manifest entry matches, push now calls writeback_create_config_in_manifest with fresh pull_hash/pull_config_hash — the same writeback the fresh-CREATE path uses. Consequences verified: the very next sync diff reads a stable entry (no re-derived adopt decision), and a later local deletion of that file is detected as deleted. Locked by a unit test asserting the on-disk manifest after push, and verified live (manifest entry restored, follow-up diff clean).
• NB-2 (gotcha entry at release time): done. gotchas.md gained a (since v0.72.0) section covering the adopted-by-id writeback alongside the rest of the sync trust cluster.
• NB-3 (E2E test for the sync push creates duplicate configs for every config a dev branch inherits from main (even with zero local changes) #482 branch-switch-then-push sequence): not included. It needs a disposable dev branch created/torn down by the harness, which the current E2E fixture set does not provide. v0.72.0 does add a new live E2E test (test_sync_theirs_reconcile_and_is_disabled) covering the adjacent trust-cluster behaviors, but the exact sync push creates duplicate configs for every config a dev branch inherits from main (even with zero local changes) #482 sequence remains manual-verified only. If you want it tracked, say the word and we split NB-3 into its own issue rather than reopening this one.