Fix update-base error when branches are fully integrated

[mtsgrd]

Summary

Fixes the error The new head names do not match the current heads that occurs when updating the workspace base after branches have been fully integrated upstream.

Problem

set_all_heads validates that the rebase output references match exactly the non-archived heads in a stack. When a branch is fully integrated, the rebaser prunes it from its output since there are no remaining commits. However, archival was happening after this validation, so the fully-integrated branch was still counted as a non-archived head — causing a mismatch between the head names and the rebase references.

Fix

• Move branch archival to run before set_heads_from_rebase_output
• Detect heads that are absent from the rebase output (i.e. branches already fully integrated with no remaining commits) and include them in the archival set

This ensures that by the time validation runs, fully-integrated branches are already marked as archived and excluded from the comparison.

[Copilot]

Pull request overview

This PR addresses a failure during “update base” when some stack heads are already fully integrated and therefore no longer show up in the rebase output, causing set_heads_from_rebase_output to reject the update due to a head/reference mismatch.

Changes:

• Moves integrated-head archival earlier in the upstream integration update flow (before set_heads_from_rebase_output).
• Expands the archival candidate set to also include non-archived stack heads that are absent from the rebase output references.
• Introduces HashSet usage to efficiently detect which heads are missing from the rebase output.

Comments suppressed due to low confidence (1)

crates/gitbutler-branch-actions/src/upstream_integration.rs:675

• Archiving heads before set_heads_from_rebase_output() can cause a new validation failure: set_all_heads() requires the rebase output’s reference names to match exactly the non-archived heads, but output.references may still include entries for heads you just archived (e.g. branches in for_archival that now have zero picks but still have RebaseStep::Reference markers). Consider filtering output.references to only those refs that correspond to stack.heads where !archived (or alternatively, only pre-archive the “missing from output” heads and keep for_archival archival after set_heads_from_rebase_output).

            // Update the branch heads
            if let Some(output) = rebase_output {
                stack.set_heads_from_rebase_output(ctx, output.references.clone())?;
            }

[Copilot]

Pull request overview

Fixes upstream integration (integrate_upstream) failing with The new head names do not match the current heads when a stack contains branches that become fully integrated (and thus are pruned from rebase output).

Changes:

• Archive integrated/pruned heads before applying rebase-output head updates during upstream integration.
• Filter rebase output references to exclude archived heads so set_all_heads validation sees a consistent active-head set.
• Add a regression test covering a stack with a fully integrated branch that should be archived instead of causing a validation error.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
crates/gitbutler-branch-actions/src/upstream_integration.rs	Archives integrated heads earlier and filters rebase references to avoid head-name mismatches during validation.
crates/gitbutler-branch-actions/tests/branch-actions/virtual_branches/apply_virtual_branch.rs	Adds a regression test reproducing the fully-integrated-branch scenario and asserting successful integration + archival.