cli: restore coverage that rode out with deleted dead wrappers

Review feedback on the dead-code sweep: two deletions took the only tests of live logic with them.

• factoryaidroid: the six subagent-aggregation tests only exercised the dead path-based twins, but the logic lives on in CalculateTotalTokenUsageFromBytes/ExtractAllModifiedFilesFromBytes — the production path via lifecycle.go, and Droid isn't in the CI canary. Retarget them at the FromBytes entry points: per-checkpoint offset math, the APICallCount>0 subagent gate, cross-agent file dedup, and missing-transcript tolerance are asserted again.
• explain: the three default-view tests only drove the deleted runExplainDefault wrappers, leaving runExplainBranchWithFilter — the real branch soph/deslop checkpoints 114

● f06be81196bf "<task-notification>\n<task-id>b53nll3s4</task-id>\n<tool-us..." 07-02 18:12 (ca82a6a) cli: drop types and test helper orphaned by the dead-code sweep

● 7307caae423f "<task-notification>\n<task-id>b53nll3s4</task-id>\n<tool-us..." 07-02 18:12 (350f6ff) cli subpackages: delete dead code and its dedicated tests

● 7c22eaba7124 "<task-notification>\n<task-id>b53nll3s4</task-id>\n<tool-us..." 07-02 18:12 (13b0ab1) cli: dedupe tmp-state cleanup and rewind preview warnings

● 8a9c75ea075f "<task-notification>\n<task-id>b53nll3s4</task-id>\n<tool-us..." 07-02 18:12 (a2c89a2) cli: delete dead root-package code and its dedicated tests

● ab0d1ee8ae62 e2e: share the run-capture/deadline-wrap block across age... 07-02 18:12 (c7443f4) e2e: share the run-capture/deadline-wrap block across agent runners

● 5eec000c7982 agent/geminicli: drop trailing blank line left by parser ... 07-02 18:12 (3ea3351) agent/geminicli: drop trailing blank line left by parser fold

● e64c28c66fb4 strategy, trailers, clusterdiscovery: delete dead code an... 07-02 18:12 (10892ce) strategy, trailers, clusterdiscovery: delete dead code and its tests

● 351ee2316125 cli: standardize on printJSON for indented JSON output 07-02 18:12 (7f9b918) cli: standardize on printJSON for indented JSON output

● 5c2527f62f77 cli: share the stop-sessions confirmation prompt 07-02 18:12 (62ea674) cli: share the stop-sessions confirmation prompt

● 76f119a87828 cli: dedupe agent display-name and hook-agent-option buil... 07-02 18:12 (a0ab634) cli: dedupe agent display-name and hook-agent-option building in setup

● 65cfea8234e1 agent/vogon: reuse one parser for the sessionInfoRaw hooks 07-02 18:12 (ff99145) agent/vogon: reuse one parser for the sessionInfoRaw hooks

● 4bfedc11ca7f review: dedupe config filtering and picker multiselect co... 07-02 18:12 (02a59b9) review: dedupe config filtering and picker multiselect construction

● 11253d4586b3 agent: dedupe transcript scanning in opencode and copilot... 07-02 18:12 (3aada34) agent: dedupe transcript scanning in opencode and copilot-cli

● 7b73bd925300 "/goal simplify this repo, make sure to de-slop it continu..." 07-02 18:11 (1b1e8b5) agent: collapse capability As* helpers onto two generic gates

● cafa646983ad [imported] "can you review https://github.com/entireio/cli/pull/1462" 07-01 13:59 (cafa646) can you review https://github.com/entireio/cli/pull/1462

● 5bc51efe5634 [imported] "could we also add "PR #1237" or "T #123" (for trail) so m..." 07-01 13:39 (5bc51ef) could we also add "PR #1237" or "T #123" (for trail) so m...

● 1686873c82fe [imported] "test" 07-01 13:33 (1686873) test

● 424e70130be4 [imported] "can you review again, did it change?" 07-01 13:19 (424e701) can you review again, did it change?

● 88b96bfc1a5c [imported] "check" 07-01 13:18 (88b96bf) check

● 67b0ce56bd73 [imported] "one" 07-01 13:18 (67b0ce5) one

● 39348f4dc708 [imported] "can you post it as finding to the trail?" 07-01 13:11 (39348f4) can you post it as finding to the trail?

● 37c58b1285cc [imported] "so it worked a few times, but now it doesn't..." 07-01 13:07 (37c58b1) so it worked a few times, but now it doesn't...

● 738da64b0dfb [imported] "can you review https://github.com/entireio/cli/pull/1573" 07-01 13:02 (738da64) can you review https://github.com/entireio/cli/pull/1573

● 42a4208d02fc [imported] "just testing if it updates now if I really type something" 07-01 12:15 (42a4208) just testing if it updates now if I really type something

● 3be2e037f80a [imported] "yes, revert" 07-01 10:46 (3be2e03) yes, revert

● 3b397151d6f6 [imported] "can you look at this comment: https://github.com/anthropi..." 07-01 10:38 (3b39715) can you look at this comment: https://github.com/anthropi...

● 4555162959cd [imported] "I think it worked when I left the focus for the window an..." 07-01 10:37 (4555162) I think it worked when I left the focus for the window an...

● 76eb3d2b9d98 [imported] "ok" 07-01 10:34 (76eb3d2) ok

● 2124a6f6a229 [imported] "test" 07-01 10:34 (2124a6f) test

● 4330123cdcf9 [imported] "it does not work :(" 06-30 16:20 (4330123) it does not work :(

● 4d9c7190f539 [imported] "ok, restarted, let's try again" 06-30 16:19 (4d9c719) ok, restarted, let's try again

● aaabdc00513b [imported] "I changed it, is this auto picked up or needs a restart?" 06-30 16:18 (aaabdc0) I changed it, is this auto picked up or needs a restart?

● 06862b0f6354 [imported] "Help me fix the issues reported by /doctor below.\n\nFor ea..." 06-30 16:16 (06862b0) Help me fix the issues reported by /doctor below.

For ea...

● 8e56c6a6b74f [imported] "I put the line into the settings.json since I briefly saw..." 06-30 16:11 (8e56c6a) I put the line into the settings.json since I briefly saw...

● 5f4910a121d0 [imported] "no" 06-30 16:07 (5f4910a) no

● 4a0d45bf06c5 [imported] "it does not, but maybe I have not title set to """ 06-30 16:05 (4a0d45b) it does not, but maybe I have not title set to ""

● a03587b3282a [imported] "works now, test" 06-30 16:04 (a03587b) works now, test

● 17e892e14dd0 [imported] "⏺ Ran 2 stop hooks\n ⎿ \u00a0Stop hook error: Failed with non-..." 06-30 16:00 (17e892e) ⏺ Ran 2 stop hooks ⎿  Stop hook error: Failed with non-...

● 9299dcc26c8e [imported] "hello" 06-30 15:59 (9299dcc) hello

● 3d591b1340c3 [imported] "Help me fix the issues reported by /doctor below.\n\nFor ea..." 06-30 15:58 (3d591b1) Help me fix the issues reported by /doctor below.

For ea...

● 32197462b83a [imported] "yeah let's try wiring the stop hook in my settings.json, ..." 06-30 15:55 (3219746) yeah let's try wiring the stop hook in my settings.json, ...

● 08301e76c817 [imported] "but it would not work with claude being in the window and..." 06-30 15:52 (08301e7) but it would not work with claude being in the window and...

● 80b129a53f56 [imported] "I'd like to show when the last "change" in a ghostty tab ..." 06-30 15:49 (80b129a) I'd like to show when the last "change" in a ghostty tab ...

● 9454bdd3f330 [imported] "this has no a conflict with the base branch" 06-30 15:01 (9454bdd) this has no a conflict with the base branch

● 0652f4abbdbb [imported] "can you look at the pr comments, and also if the correspo..." 06-30 14:29 (0652f4a) can you look at the pr comments, and also if the correspo...

● f842b0ae13c4 [imported] "yes, do that" 06-30 14:07 (f842b0a) yes, do that

● aff3a8f7636f [imported] "did we open a PR yet?" 06-30 14:06 (aff3a8f) did we open a PR yet?

● 642544e41c50 [imported] "- cmd/entire/cli/paths/paths.go:32 still says transcript...." 06-30 12:28 (642544e) - cmd/entire/cli/paths/paths.go:32 still says transcript....

● 03570057e87a [imported] "- P2 cmd/entire/cli/transcript/compact/compact.go:158: Fu..." 06-30 11:42 (0357005) - P2 cmd/entire/cli/transcript/compact/compact.go:158: Fu...

● d0b9faddc75d [imported] "<task-notification>\n<task-id>a0b8ca16f3d36a411</task-id>\n..." 06-30 11:15 (d0b9fad) <task-notification> <task-id>a0b8ca16f3d36a411</task-id> ...

● 9b2eb8b87c47 [imported] "<task-notification>\n<task-id>a78ca6485d1be4ff7</task-id>\n..." 06-30 11:14 (9b2eb8b) <task-notification> <task-id>a78ca6485d1be4ff7</task-id> ...

● 9c84afa51639 [imported] "<task-notification>\n<task-id>a457acc7c9d47e06e</task-id>\n..." 06-30 11:14 (9c84afa) <task-notification> <task-id>a457acc7c9d47e06e</task-id> ...

● 76b715ce095f [imported] "/simplify → 4 cleanup agents in parallel → apply the fix..." 06-30 11:12 (76b715c) /simplify → 4 cleanup agents in parallel → apply the fix...

● 4877690ab239 [imported] "how could 2 even work, we don't write the checkpoints at ..." 06-30 09:23 (4877690) how could 2 even work, we don't write the checkpoints at ...

● 2bc7d831d62e [imported] "can we start working on this?" 06-30 09:09 (2bc7d83) can we start working on this?

● d2b6c31a4e9b [imported] "Yeah but the issue is as soon as a checkpoint / commit in..." 06-30 08:57 (d2b6c31) Yeah but the issue is as soon as a checkpoint / commit in...

● def9943b30f0 [imported] "if we would want to store the transcript.jsonl as full we..." 06-30 08:46 (def9943) if we would want to store the transcript.jsonl as full we...

● 058751630ccb [imported] "<task-notification>\n<task-id>a676a8185d76c1abe</task-id>\n..." 06-30 08:42 (0587516) <task-notification> <task-id>a676a8185d76c1abe</task-id> ...

● 66311ee49b8c [imported] "can you give me a summary how we store session logs right..." 06-30 08:40 (66311ee) can you give me a summary how we store session logs right...

● e698e190b41c [imported] "can you also post the findings on 1472" 06-29 16:23 (e698e19) can you also post the findings on 1472

● acd45beca109 [imported] "can you post those as findings on the trail using the cli..." 06-29 15:34 (acd45be) can you post those as findings on the trail using the cli...

● 4ffd98acbcbe [imported] "can you review https://github.com/entireio/cli/pull/1313" 06-29 15:25 (4ffd98a) can you review https://github.com/entireio/cli/pull/1313

● e16e3aaaac83 [imported] "can you review https://github.com/entireio/cli/pull/1472" 06-29 13:34 (e16e3aa) can you review https://github.com/entireio/cli/pull/1472

● 1b18c7ec130e [imported] "can you review again, I rebased" 06-29 13:12 (1b18c7e) can you review again, I rebased

● 9ad2a22d8dfc [imported] "can you review https://github.com/entireio/cli/pull/1549 ..." 06-29 12:22 (9ad2a22) can you review https://github.com/entireio/cli/pull/1549 ...

● 06efd7549b2f [imported] "I also not sure I like the design choice of just "public"..." 06-29 11:52 (06efd75) I also not sure I like the design choice of just "public"...

● a090f0dc130b [imported] "can you review https://github.com/entireio/cli/pull/1531 ..." 06-29 11:26 (a090f0d) can you review https://github.com/entireio/cli/pull/1531 ...

● 9a01b7c38400 [imported] "ok, now update the other place for the brew docs :)" 06-29 10:08 (9a01b7c) ok, now update the other place for the brew docs :)

● c7139bb53c2b [imported] "can you first review 1529 again" 06-29 10:03 (c7139bb) can you first review 1529 again

● 6a72ca55142f [imported] "back to 1534: can you check there are not other places wh..." 06-29 09:59 (6a72ca5) back to 1534: can you check there are not other places wh...

● 9d5af71d1933 [imported] "can you now review https://github.com/entireio/cli/pull/1529" 06-29 09:50 (9d5af71) can you now review https://github.com/entireio/cli/pull/1529

● 474fa98bdd8d [imported] "can you look at https://github.com/entireio/cli/pull/1534..." 06-29 09:45 (474fa98) can you look at https://github.com/entireio/cli/pull/1534...

● 4f8c1a05c7b7 [imported] "can you post the findings to the trail" 06-26 10:51 (4f8c1a0) can you post the findings to the trail

● a30148800f79 [imported] "<task-notification>\n<task-id>acb9f26eddbbec259</task-id>\n..." 06-26 09:49 (a301488) <task-notification> <task-id>acb9f26eddbbec259</task-id> ...

● 52143da192be [imported] "<task-notification>\n<task-id>a8ef47f97666c7ec7</task-id>\n..." 06-26 09:47 (52143da) <task-notification> <task-id>a8ef47f97666c7ec7</task-id> ...

● cb6566b53cf4 [imported] "<task-notification>\n<task-id>ab560e36ee1d3b4fe</task-id>\n..." 06-26 09:46 (cb6566b) <task-notification> <task-id>ab560e36ee1d3b4fe</task-id> ...

● 0b6374e0727b [imported] "can you now review https://entire.io/gh/entireio/cli/trai..." 06-26 09:34 (0b6374e) can you now review https://entire.io/gh/entireio/cli/trai...

● 3780222c8dca [imported] "can you post the two findings on the corespoding trail?" 06-26 09:33 (3780222) can you post the two findings on the corespoding trail?

● 17a5bc98ead8 [imported] "<task-notification>\n<task-id>ab980f2b645d399d7</task-id>\n..." 06-26 09:05 (17a5bc9) <task-notification> <task-id>ab980f2b645d399d7</task-id> ...

● e3746a86fc59 [imported] "can you review https://entire.io/gh/entireio/cli/trails/6..." 06-26 08:55 (e3746a8) can you review https://entire.io/gh/entireio/cli/trails/6...

● da9f546ca0b2 [imported] "can you review https://github.com/entireio/cli/pull/1511 ..." 06-26 07:15 (da9f546) can you review https://github.com/entireio/cli/pull/1511 ...

● d7db80fe900d [imported] "How can we figure out the checkpoint version before talki..." 06-25 17:45 (d7db80f) How can we figure out the checkpoint version before talki...

● 60a30c517d1d [imported] "can you check https://github.com/entireio/cli/pull/1507 i..." 06-25 17:28 (60a30c5) can you check https://github.com/entireio/cli/pull/1507 i...

● 4de09c8dbe06 [imported] "are you sure the other code isn't generated too?" 06-25 13:46 (4de09c8) are you sure the other code isn't generated too?

● a7f2ccdfdae6 [imported] "<task-notification>\n<task-id>a5eabac878feb054a</task-id>\n..." 06-25 12:47 (a7f2ccd) <task-notification> <task-id>a5eabac878feb054a</task-id> ...

● ae405e941044 [imported] "<task-notification>\n<task-id>a81ae07c29c11807f</task-id>\n..." 06-25 12:46 (ae405e9) <task-notification> <task-id>a81ae07c29c11807f</task-id> ...

● 074a9669b87b [imported] "can you review https://github.com/entireio/cli/pull/1518 ..." 06-25 12:41 (074a966) can you review https://github.com/entireio/cli/pull/1518 ...

● aac680e5d19a [imported] "can you review https://entire.io/gh/entireio/cli/trails/661" 06-25 11:35 (aac680e) can you review https://entire.io/gh/entireio/cli/trails/661

● d7f57fda979d [imported] "can you review https://entire.io/gh/entireio/cli/trails/652/" 06-25 10:29 (d7f57fd) can you review https://entire.io/gh/entireio/cli/trails/652/

● a0dc8c4fe795 [imported] "can you review https://github.com/entireio/cli/pull/1499 ..." 06-25 10:05 (a0dc8c4) can you review https://github.com/entireio/cli/pull/1499 ...

● 4991964f4c59 [imported] "Add debug" 06-25 09:13 (4991964) Add debug

● 3889f0ebbc6a [imported] "Ok. Sounds good. The only thing I‘m now still wondering: ..." 06-25 09:11 (3889f0e) Ok. Sounds good. The only thing I‘m now still wondering: ...

● 908a3544dda7 [imported] "can you explain to me when resume will now directly launc..." 06-25 06:45 (908a354) can you explain to me when resume will now directly launc...

● b257152616fa [imported] "can you check again, there were some new commits" 06-25 06:29 (b257152) can you check again, there were some new commits

● d1772ae84a2c [imported] "The issue is: we are writing the placeholders - but they ..." 06-25 06:26 (d1772ae) The issue is: we are writing the placeholders - but they ...

● 5fd4acd71e1f [imported] "Hmm. It has none merged. The prior try failed because no ..." 06-24 16:19 (5fd4acd) Hmm. It has none merged. The prior try failed because no ...

● f2b9c1baea12 [imported] "Hmm. It has none merged. The prior try failed because no ..." 06-24 14:53 (f2b9c1b) Hmm. It has none merged. The prior try failed because no ...

● 15cbecef4326 [imported] "Question: but the skipping sounds as if no new prompts we..." 06-24 14:50 (15cbece) Question: but the skipping sounds as if no new prompts we...

● a5355b1b65c9 [imported] "[Request interrupted by user for tool use]" 06-24 14:50 (a5355b1) [Request interrupted by user for tool use]

● b99b7a61ff82 [imported] "Question: but the skipping sounds as if no new prompts we..." 06-24 14:33 (b99b7a6) Question: but the skipping sounds as if no new prompts we...

● 9e3847afcfc2 [imported] "can you take a look at this, I did run it in ../git-sync:..." 06-24 14:16 (9e3847a) can you take a look at this, I did run it in ../git-sync:...

● caabf544820c [imported] "<task-notification>\n<task-id>a3074a8a47b891551</task-id>\n..." 06-24 14:03 (caabf54) <task-notification> <task-id>a3074a8a47b891551</task-id> ...

● 6c110eac3ed6 [imported] "<task-notification>\n<task-id>a13dc9fa412edcc6e</task-id>\n..." 06-24 14:03 (6c110ea) <task-notification> <task-id>a13dc9fa412edcc6e</task-id> ...

● 75f953bc7f73 [imported] "<task-notification>\n<task-id>ad20ef831ab9e65ac</task-id>\n..." 06-24 14:02 (75f953b) <task-notification> <task-id>ad20ef831ab9e65ac</task-id> ...

● 6a06d3d60b75 [imported] "<task-notification>\n<task-id>ab0dd083f555810c5</task-id>\n..." 06-24 14:02 (6a06d3d) <task-notification> <task-id>ab0dd083f555810c5</task-id> ...

● 9919dc6061ec [imported] "/simplify → 4 cleanup agents in parallel → apply the fix..." 06-24 13:58 (9919dc6) /simplify → 4 cleanup agents in parallel → apply the fix...

● 87e140dbb789 [imported] "<task-notification>\n<task-id>a574469aa1c7a2156</task-id>\n..." 06-24 13:47 (87e140d) <task-notification> <task-id>a574469aa1c7a2156</task-id> ...

● d88c60c7e9d5 [imported] "<task-notification>\n<task-id>abcc3502034cdc607</task-id>\n..." 06-24 13:43 (d88c60c) <task-notification> <task-id>abcc3502034cdc607</task-id> ...

● 3513316e30da [imported] "hmm, they are embedded with the long prompts we have on m..." 06-24 13:38 (3513316) hmm, they are embedded with the long prompts we have on m...

● d60960deb068 [imported] "can you review https://github.com/entireio/cli/pull/1511 ..." 06-24 13:33 (d60960d) can you review https://github.com/entireio/cli/pull/1511 ...

● d30159d49f5f [imported] "can you add both as findings to the trail" 06-24 13:22 (d30159d) can you add both as findings to the trail

● 9c5d56031982 [imported] "<task-notification>\n<task-id>ab0220103d4f0fce1</task-id>\n..." 06-24 13:20 (9c5d560) <task-notification> <task-id>ab0220103d4f0fce1</task-id> ...

● 97e388529f33 [imported] "can you also look at https://entire.io/gh/entireio/cli/tr..." 06-24 13:15 (97e3885) can you also look at https://entire.io/gh/entireio/cli/tr...

● 61404c98152c [imported] "ok, I think we need to change the onboarding idea a bit. ..." 06-24 13:04 (61404c9) ok, I think we need to change the onboarding idea a bit. ... path — unasserted. Retarget them (branch view, zero-checkpoint hint, detached-HEAD labeling) with the wrapper's implied no-filter arguments, sharing one setup helper instead of the original copy-pasted scaffolding.