Encara que el sender és llarg, arribarem al refugi.

Encara que means although / even though. It introduces a contrast:

• Encara que el sender és llarg = Although the path is long
• arribarem al refugi = we will arrive at the refuge / mountain hut

It works like English although at the start of a sentence.

Because que by itself usually means that, which, or than, depending on the context.
The full expression encara que is a fixed conjunction meaning although / even if.

So:

• que = many possible meanings
• encara que = a specific connector meaning although / even though

Because sender is a masculine noun in Catalan, so it takes the masculine article el:

• el sender = the path / trail

This is something learners usually have to memorize with the noun. Not all nouns match English expectations for gender.

Both can refer to a path or way, but sender usually suggests a trail or footpath, especially in nature or the mountains.
Camí is a more general word for path, way, road, track.

So in a hiking context, sender fits very naturally.

És is the 3rd person singular present of ser (to be):

• el sender és llarg = the path is long

It agrees with el sender, which is singular.

Because adjectives in Catalan usually agree with the noun in gender and number.

• sender is masculine singular
• so the adjective is llarg (masculine singular)

Compare:

• el sender llarg = the long path
• la ruta llarga = the long route

Arribarem is the 1st person plural future of arribar (to arrive):

• arribaré = I will arrive
• arribarem = we will arrive

It is used because the sentence refers to a future result: we will arrive at the refuge.

Because arribar normally uses the preposition a before a destination:

• arribar a
  • place = to arrive at a place

Since a + el contracts to al, we get:

• a + el refugi → al refugi

So:

• arribarem al refugi = we will arrive at the refuge

Yes, in normal standard Catalan:

• a + el → al
• de + el → del

Examples:

• vaig al poble = I’m going to the village
• venim del poble = we come from the village

But this contraction only happens with el, not with all articles.

The comma separates the subordinate clause introduced by encara que from the main clause:

• Encara que el sender és llarg, = subordinate concessive clause
• arribarem al refugi. = main clause

This is very similar to English punctuation with although at the start of a sentence.

Yes. Depending on context, encara que can mean either:

• although / even though when the fact is presented as real
• even if when it is more hypothetical

In your sentence, it sounds like although / even though, because the path being long is treated as a real fact.

After encara que, Catalan can use either the indicative or the subjunctive, depending on meaning.

Here, és is indicative because the speaker presents the path being long as a known fact:

• Encara que el sender és llarg... = Although the path is long...

If the idea were more uncertain or hypothetical, Catalan could use the subjunctive instead.

Yes. Catalan word order is flexible here. You could also say:

• Arribarem al refugi, encara que el sender és llarg.

That means the same thing.
Starting with encara que puts more emphasis on the contrast first.