Made wider use of flatpak_repo_resolve_rev()

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As described in the last commit message, it makes sense to move toward
using flatpak_repo_resolve_rev() rather than ostree_repo_resolve_rev()
for a few reasons:
1) It means we can use OSTREE_REPO_PULL_FLAGS_MIRROR which causes refs
to be pulled into repo/refs/mirrors/ rather than repo/refs/remotes/
which fixes a few edge cases of using collection IDs[1]
2) It falls back to using ostree_repo_resolve_rev() if
ostree_repo_resolve_collection_ref() fails so we can maintain backwards
compatibility for repo/refs/remotes/
3) It distinguishes between remote and local refs, and in the local case
uses OSTREE_REPO_RESOLVE_REV_EXT_LOCAL_ONLY and
ostree_repo_resolve_rev_ext() to make sure we don't for example
accidentally use a remote's repo metadata rather than the local repo's
metadata for the "flatpak repo" command.

So this commit changes every instance of ostree_repo_resolve_rev() in
the codebase to flatpak_repo_resolve_rev().

[1] https://github.com/flatpak/flatpak/issues/1832

Closes: #2705
Approved by: alexlarsson

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