Deinde magistra rogat quae via commodior sit, semita ad vadum an limes ad pontem.

Quae means which here, and it agrees with via.

• via is feminine singular
• so the interrogative word must also be feminine singular: quae via
• literally: which road / route

This is not a relative pronoun here. It is introducing an indirect question: quae via commodior sit = which route is more convenient.

Because quae via commodior sit is an indirect question after rogat.

Latin normally uses the subjunctive in indirect questions:

• direct question: quae via commodior est? = Which route is more convenient?
• indirect question: magistra rogat quae via commodior sit = the teacher asks which route is more convenient

So sit is the present subjunctive of esse.

Via is nominative singular.

It is the subject of sit inside the indirect question:

• quae via commodior sit
  = which route is more convenient

The thing being described as more convenient is via, so it stands in the nominative.

Commodior is the comparative of commodus, meaning more convenient, more suitable, or easier.

It agrees with via, but comparative adjectives in Latin use third-declension endings:

• masculine/feminine nominative singular: commodior
• neuter nominative singular: commodius

Since via is feminine singular, commodior is the correct form. The form looks the same as the masculine, which is normal for comparatives.

Here an means or in a choice between two alternatives.

The two options are:

• semita ad vadum = the path to the ford
• limes ad pontem = the track/path to the bridge

So the sentence is asking which route is better: this one or that one.

In Latin, an is commonly used in alternative questions, especially after an expressed first option.

Yes, you can think of an understood utrum if that helps.

Latin often uses:

• utrum ... an ... = whether ... or ...

Here the sentence gives the first option directly and then adds an before the second, so utrum is not necessary:

• quae via commodior sit, semita ad vadum an limes ad pontem

In fuller terms, the sense is: which route is more convenient, whether the path to the ford or the track to the bridge.

Because they are the two possible answers to quae via ... sit.

They are the alternative routes being considered:

• semita = path
• limes = track / lane / boundary path

Since they correspond to the route that would be the subject of sit, they appear in the nominative as well.

You can mentally expand it like this:

• semita ad vadum [sit]
• an limes ad pontem [sit]

Because ad takes the accusative.

• ad vadum = to the ford
• ad pontem = to the bridge

This use of ad shows direction or destination.

So:

• vadum is accusative singular after ad
• pontem is accusative singular after ad

The verb is not really missing; it is simply not repeated.

The clause already has sit, and Latin often leaves a repeated verb understood. So the end of the sentence means:

• semita ad vadum [sit]
• an limes ad pontem [sit]

English does the same sort of thing: which route is more convenient, the path to the ford or the track to the bridge.

They are related, but not identical:

• via = a general road, way, or route
• semita = a narrow path or footpath
• limes = originally a boundary line, but it can also mean a track, path, or lane, especially along a boundary

In this sentence, via is the general category: which route.
Then semita and limes name the two specific possibilities.

Because Latin word order is flexible, and this order is perfectly natural.

The sentence first gives the main indirect question:

• magistra rogat quae via commodior sit

Then it adds the two alternatives as clarification:

• semita ad vadum an limes ad pontem

So the structure is roughly:

• The teacher asks which route is more convenient
• — the path to the ford or the track to the bridge.

Latin often places clarifying or balancing alternatives after the main clause or sub-clause.

Rogat means asks.

It is from rogare. In this sentence it introduces the indirect question:

• magistra rogat ... = the teacher asks ...

So the whole sentence is built around: Then the teacher asks which route is more convenient...

Deinde means then, next, or after that.

It is simply moving the narrative forward. It tells you that this question comes after something else in the story.

So:

• Deinde = Then / Next
• magistra rogat = the teacher asks